- PDB-2px4: Crystal structure of the Murray Valley Encephalitis Virus NS5 2'-... -
+
データを開く
IDまたはキーワード:
読み込み中...
-
基本情報
登録情報
データベース: PDB / ID: 2px4
タイトル
Crystal structure of the Murray Valley Encephalitis Virus NS5 2'-O Methyltransferase domain in complex with SAH (Monoclinic form 2)
要素
Genome polyprotein [Contains: Capsid protein C (Core protein); Envelope protein M (Matrix protein); Major envelope protein E; Non-structural protein 1 (NS1); Non-structural protein 2A (NS2A); Flavivirin protease NS2B regulatory subunit; Flavivirin protease NS3 catalytic subunit; Non-structural protein 4A (NS4A); Non-structural protein 4B (NS4B); RNA-directed RNA polymerase (EC 2.7.7.48) (NS5)]
キーワード
TRANSFERASE (転移酵素) / Murray Valley Encephalitis Virus / Methyltransferase (メチルトランスフェラーゼ) / SAH / Structural Genomics (構造ゲノミクス) / Oxford Protein Production Facility (オックスフォード) / OPPF
機能・相同性
機能・相同性情報
フラビビリン / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / カプシド / nucleoside-triphosphate phosphatase / double-stranded RNA binding / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity ...フラビビリン / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / カプシド / nucleoside-triphosphate phosphatase / double-stranded RNA binding / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / protein dimerization activity / ヘリカーゼ / induction by virus of host autophagy / RNA依存性RNAポリメラーゼ / viral RNA genome replication / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / エンベロープ (ウイルス) / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / virion attachment to host cell / virion membrane / structural molecule activity / ATP hydrolysis activity / タンパク質分解 / extracellular region / ATP binding / 生体膜 / metal ion binding 類似検索 - 分子機能
: / Flavivirus envelope glycoprotein E, stem/anchor domain / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus capsid protein C superfamily / : / Flavivirus non-structural protein NS2B / Flavivirus NS3 helicase, C-terminal helical domain / Genome polyprotein, Flavivirus / Flavivirus non-structural protein NS4A ...: / Flavivirus envelope glycoprotein E, stem/anchor domain / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus capsid protein C superfamily / : / Flavivirus non-structural protein NS2B / Flavivirus NS3 helicase, C-terminal helical domain / Genome polyprotein, Flavivirus / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A / Flavivirus NS2B domain profile. / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. / Flavivirus non-structural protein NS2A / Flavivirus non-structural protein NS2A / Flavivirus NS3, petidase S7 / Peptidase S7, Flavivirus NS3 serine protease / Flavivirus NS3 protease (NS3pro) domain profile. / Envelope glycoprotein M, flavivirus / Flavivirus envelope glycoprotein M / RNA-directed RNA polymerase, flavivirus / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Envelope glycoprotein M superfamily, flavivirus / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / Ribosomal RNA methyltransferase, FtsJ domain / FtsJ-like methyltransferase / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / DEAD box, Flavivirus / Flavivirus DEAD domain / Vaccinia Virus protein VP39 / helicase superfamily c-terminal domain / Immunoglobulin E-set / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase / ロスマンフォールド / 3-Layer(aba) Sandwich / Alpha Beta 類似検索 - ドメイン・相同性
HETEROGEN AUTHORS STATE THAT THE UNKNOWN ATOMS UNX801-UNX809 MARK THE POSITION IN ELECTRON DENSITY ... HETEROGEN AUTHORS STATE THAT THE UNKNOWN ATOMS UNX801-UNX809 MARK THE POSITION IN ELECTRON DENSITY AND BELONG TO AN UNKNOWN CHEMICAL GROUP.
解像度: 2.2→26.44 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.908 / SU B: 10.128 / SU ML: 0.141 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / ESU R: 0.283 / ESU R Free: 0.218 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. CNS program has also been used in refinement
Rfactor
反射数
%反射
Selection details
Rfree
0.22927
676
4.9 %
RANDOM
Rwork
0.16138
-
-
-
obs
0.16463
13226
96.39 %
-
溶媒の処理
イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.2 Å / 溶媒モデル: BABINET MODEL WITH MASK
原子変位パラメータ
Biso mean: 32.592 Å2
Baniso -1
Baniso -2
Baniso -3
1-
1.72 Å2
0 Å2
1.95 Å2
2-
-
-0.9 Å2
0 Å2
3-
-
-
0.86 Å2
精密化ステップ
サイクル: LAST / 解像度: 2.2→26.44 Å
タンパク質
核酸
リガンド
溶媒
全体
原子数
2074
0
79
180
2333
拘束条件
Refine-ID
タイプ
Dev ideal
Dev ideal target
数
X-RAY DIFFRACTION
r_bond_refined_d
0.007
0.022
2177
X-RAY DIFFRACTION
r_bond_other_d
0.002
0.02
1555
X-RAY DIFFRACTION
r_angle_refined_deg
1.037
1.992
2930
X-RAY DIFFRACTION
r_angle_other_deg
0.78
3
3754
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
4.7
5
259
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
33.77
22.632
95
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
12.273
15
395
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
15.01
15
22
X-RAY DIFFRACTION
r_chiral_restr
0.059
0.2
302
X-RAY DIFFRACTION
r_gen_planes_refined
0.003
0.02
2345
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
445
X-RAY DIFFRACTION
r_nbd_refined
0.183
0.2
424
X-RAY DIFFRACTION
r_nbd_other
0.182
0.2
1634
X-RAY DIFFRACTION
r_nbtor_refined
0.172
0.2
1025
X-RAY DIFFRACTION
r_nbtor_other
0.081
0.2
1107
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.151
0.2
145
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.177
0.2
10
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.234
0.2
47
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.172
0.2
17
X-RAY DIFFRACTION
r_mcbond_it
3.501
4
1690
X-RAY DIFFRACTION
r_mcbond_other
0.896
4
539
X-RAY DIFFRACTION
r_mcangle_it
3.701
6
2072
X-RAY DIFFRACTION
r_scbond_it
5.505
6
1056
X-RAY DIFFRACTION
r_scangle_it
7.276
10
858
LS精密化 シェル
解像度: 2.2→2.257 Å / Total num. of bins used: 20
Rfactor
反射数
%反射
Rfree
0.221
40
-
Rwork
0.16
753
-
obs
-
-
75.17 %
精密化 TLS
手法: refined / Origin x: 9.835 Å / Origin y: -0.077 Å / Origin z: 20.913 Å