5MJ4

INTERLEUKIN-23 COMPLEX WITH AN ANTAGONISTIC ALPHABODY, CRYSTAL FORM 2

4OG9」から置き換えられました

> 概要

5MJ4 の概要

関連構造のPDB ID5MJ3
分子名称Interleukin-12 subunit beta, Interleukin-23 subunit alpha, ALPHABODY MA12
機能のキーワードsingle-chain antiparallel triple-helix coiled-coil, immunoglobulin-like, 4-alpha helical bundle, antagonist, n-linked glycosylation, cytokine-antagonist complex, immune system
由来する生物種Homo sapiens (Human)
詳細
細胞内の位置Secreted P29460 Q9NPF7
ポリマー鎖数3
分子量合計67423.71
構造登録者
主引用文献
Desmet, J.,Verstraete, K.,Bloch, Y.,Lorent, E.,Wen, Y.,Devreese, B.,Vandenbroucke, K.,Loverix, S.,Hettmann, T.,Deroo, S.,Somers, K.,Henderikx, P.,Lasters, I.,Savvides, S.
STRUCTURAL BASIS OF IL-23 ANTAGONISM BY AN ALPHABODY PROTEIN
Nature Communications, 5:5237-, 2014
PubMed: 25354530
DOI: 10.1038/NCOMMS6237
MImport into Mendeley
実験手法
X-RAY DIFFRACTION (3.4 Å)
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構造検証レポート

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.29131.2%0.7%8.1%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution
検証レポート(詳細版)をダウンロード

他の静止画像(非対称単位)

Molmil generated image of 5mj4
回転なし
Molmil generated image of 5mj4
x軸(左右方向)周りに90°回転
Molmil generated image of 5mj4
y軸(上下方向)周りに90°回転

> 構造情報

エンティティ

鎖名説明種類鎖長分子量分子数データベース名(アクセス番号)由来する生物種エンティティの一般名
AInterleukin-12 subunit betapolymer30634739.91
UniProt (P29460)
Pfam (PF10420)
Homo sapiens (Human)IL-12B,Cytotoxic lymphocyte maturation factor 40 kDa subunit,CLMF p40,IL-12 subunit p40,NK cell stimulatory factor chain 2,NKSF2
BInterleukin-23 subunit alphapolymer17919812.31
UniProt (Q9NPF7)
Pfam (PF16649)
Homo sapiens (Human)IL-23-A,Interleukin-23 subunit p19,IL-23p19
CALPHABODY MA12polymer11811888.51
synthetic construct
N-ACETYL-D-GLUCOSAMINEnon-polymer221.22
BETA-D-MANNOSEnon-polymer180.21
ALPHA-D-MANNOSEnon-polymer180.22

配列ビューア

非対称単位の内容

ポリマー鎖の数3
分子量合計66440.8
非ポリマー*分子数5
分子量合計982.9
全て*分子量合計67423.7
*水分子は含んでいません

> 実験情報

精密化の統計情報

実験手法:X-RAY DIFFRACTION (3.4 Å)

格子定数 [Å]57.85057.850366.480
格子定数 [度]90.0090.0090.00
空間群P 41 21 2
分解能 [Å] (低 - 高)57.00 - 3.40
最も高い分解能シェルの値3.569 - 3.391
R因子0.2584
R-work0.25470
最も高い分解能シェルの値0.319
R-free0.29590
最も高い分解能シェルの値0.368
結合長の平均二乗偏差(RMSD) [Å]0.004
結合角の平均二乗偏差(RMSD) [度]0.850

回折データの統計情報

分解能 [Å] (低 - 高)57.00 - 3.40
最も高い分解能シェルの値 -
独立反射数9551
完全性 [%]99.9
冗長性22.29
最も高い分解能シェルの値23.4

結晶化条件

結晶ID方法pHpHの範囲温度単位
1VAPOR DIFFUSION, SITTING DROP7.3294

結晶化試薬

ID結晶ID濃度試薬名濃度 (単位)詳細
文献の結晶化試薬*
ID結晶ID溶液試薬名濃度 (単位) (単位)詳細
注釈情報は下記文献より抽出しています*

> 機能情報

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GO(遺伝子オントロジー)由来の情報

鎖名GO(遺伝子オントロジー)id名前空間内容
A0005737cellular_componentcytoplasm
A0005576cellular_componentextracellular region
A0005615cellular_componentextracellular space
A0043514cellular_componentinterleukin-12 complex
A0070743cellular_componentinterleukin-23 complex
A0016020cellular_componentmembrane
A0004896molecular_functioncytokine receptor activity
A0042802molecular_functionidentical protein binding
A0042164molecular_functioninterleukin-12 alpha subunit binding
A0005143molecular_functioninterleukin-12 receptor binding
A0046982molecular_functionprotein heterodimerization activity
A0007050biological_processcell cycle arrest
A0016477biological_processcell migration
A0071346biological_processcellular response to interferon-gamma
A0071222biological_processcellular response to lipopolysaccharide
A0050829biological_processdefense response to Gram-negative bacterium
A0042832biological_processdefense response to protozoan
A0051607biological_processdefense response to virus
A0042095biological_processinterferon-gamma biosynthetic process
A0030101biological_processnatural killer cell activation
A0002323biological_processnatural killer cell activation involved in immune response
A0044130biological_processnegative regulation of growth of symbiont in host
A0002862biological_processnegative regulation of inflammatory response to antigenic stimulus
A0032693biological_processnegative regulation of interleukin-10 production
A0032700biological_processnegative regulation of interleukin-17 production
A0048662biological_processnegative regulation of smooth muscle cell proliferation
A0042104biological_processpositive regulation of activated T cell proliferation
A0010535biological_processpositive regulation of activation of JAK2 kinase activity
A0045785biological_processpositive regulation of cell adhesion
A0002230biological_processpositive regulation of defense response to virus by host
A0032725biological_processpositive regulation of granulocyte macrophage colony-stimulating factor production
A0050729biological_processpositive regulation of inflammatory response
A0045078biological_processpositive regulation of interferon-gamma biosynthetic process
A0032729biological_processpositive regulation of interferon-gamma production
A0032733biological_processpositive regulation of interleukin-10 production
A0032735biological_processpositive regulation of interleukin-12 production
A0032740biological_processpositive regulation of interleukin-17 production
A0050671biological_processpositive regulation of lymphocyte proliferation
A0043382biological_processpositive regulation of memory T cell differentiation
A0032946biological_processpositive regulation of mononuclear cell proliferation
A0032816biological_processpositive regulation of natural killer cell activation
A0002860biological_processpositive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target
A0032819biological_processpositive regulation of natural killer cell proliferation
A0042346biological_processpositive regulation of NF-kappaB import into nucleus
A0051135biological_processpositive regulation of NK T cell activation
A0051142biological_processpositive regulation of NK T cell proliferation
A0045672biological_processpositive regulation of osteoclast differentiation
A0034393biological_processpositive regulation of smooth muscle cell apoptotic process
A0001916biological_processpositive regulation of T cell mediated cytotoxicity
A0042102biological_processpositive regulation of T cell proliferation
A0002827biological_processpositive regulation of T-helper 1 type immune response
A2000330biological_processpositive regulation of T-helper 17 cell lineage commitment
A2000318biological_processpositive regulation of T-helper 17 type immune response
A0034105biological_processpositive regulation of tissue remodeling
A0032760biological_processpositive regulation of tumor necrosis factor production
A0042517biological_processpositive regulation of tyrosine phosphorylation of Stat3 protein
A0042520biological_processpositive regulation of tyrosine phosphorylation of Stat4 protein
A0042523biological_processpositive regulation of tyrosine phosphorylation of Stat5 protein
A0042035biological_processregulation of cytokine biosynthetic process
A0042510biological_processregulation of tyrosine phosphorylation of Stat1 protein
A0010224biological_processresponse to UV-B
A0019233biological_processsensory perception of pain
A0019953biological_processsexual reproduction
A0042088biological_processT-helper 1 type immune response
A0042093biological_processT-helper cell differentiation
B0005576cellular_componentextracellular region
B0070743cellular_componentinterleukin-23 complex
B0050829biological_processdefense response to Gram-negative bacterium
B0051607biological_processdefense response to virus
B0006954biological_processinflammatory response
B0045087biological_processinnate immune response
B0032693biological_processnegative regulation of interleukin-10 production
B0042104biological_processpositive regulation of activated T cell proliferation
B0010535biological_processpositive regulation of activation of JAK2 kinase activity
B0002230biological_processpositive regulation of defense response to virus by host
B0032725biological_processpositive regulation of granulocyte macrophage colony-stimulating factor production
B0050729biological_processpositive regulation of inflammatory response
B0032729biological_processpositive regulation of interferon-gamma production
B0032733biological_processpositive regulation of interleukin-10 production
B0032735biological_processpositive regulation of interleukin-12 production
B0032740biological_processpositive regulation of interleukin-17 production
B0043382biological_processpositive regulation of memory T cell differentiation
B0032816biological_processpositive regulation of natural killer cell activation
B0032819biological_processpositive regulation of natural killer cell proliferation
B0090023biological_processpositive regulation of neutrophil chemotaxis
B0042346biological_processpositive regulation of NF-kappaB import into nucleus
B0051135biological_processpositive regulation of NK T cell activation
B0051142biological_processpositive regulation of NK T cell proliferation
B0045672biological_processpositive regulation of osteoclast differentiation
B0001916biological_processpositive regulation of T cell mediated cytotoxicity
B0042102biological_processpositive regulation of T cell proliferation
B0002827biological_processpositive regulation of T-helper 1 type immune response
B2000330biological_processpositive regulation of T-helper 17 cell lineage commitment
B2000318biological_processpositive regulation of T-helper 17 type immune response
B0034105biological_processpositive regulation of tissue remodeling
B0045944biological_processpositive regulation of transcription from RNA polymerase II promoter
B0032760biological_processpositive regulation of tumor necrosis factor production
B0042517biological_processpositive regulation of tyrosine phosphorylation of Stat3 protein
B0042520biological_processpositive regulation of tyrosine phosphorylation of Stat4 protein
B0042523biological_processpositive regulation of tyrosine phosphorylation of Stat5 protein
B0042510biological_processregulation of tyrosine phosphorylation of Stat1 protein
B0042098biological_processT cell proliferation
B0048771biological_processtissue remodeling
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PDBデータベースに由来する情報

site_id残基数詳細
AC15binding site for Poly-Saccharide residues NAG A 500 through MAN A 504 bound to ASN A 222
鎖名残基
ATRP24
AGLU34
AHIS105
ATYR220
AASN222

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「HETATM」原子の座標から抽出されたリガンド結合部位

site_id残基数詳細
NAG_5mj4_A_5014N-ACETYL-D-GLUCOSAMINE binding site
鎖名残基ligand
ATRP24-GLU25NAG: N-ACETYL-D-GLUCOSAMINE
AGLU34NAG: N-ACETYL-D-GLUCOSAMINE
ATRP112NAG: N-ACETYL-D-GLUCOSAMINE

BMA_5mj4_A_5022BETA-D-MANNOSE binding site
鎖名残基ligand
ATRP24-GLU25BMA: BETA-D-MANNOSE

NAG_5mj4_A_50011N-ACETYL-D-GLUCOSAMINE binding site
鎖名残基ligand
ATRP24NAG: N-ACETYL-D-GLUCOSAMINE
ALEU26NAG: N-ACETYL-D-GLUCOSAMINE
AVAL32NAG: N-ACETYL-D-GLUCOSAMINE
AGLU34NAG: N-ACETYL-D-GLUCOSAMINE
AHIS105NAG: N-ACETYL-D-GLUCOSAMINE
ATRP112NAG: N-ACETYL-D-GLUCOSAMINE
ALYS157NAG: N-ACETYL-D-GLUCOSAMINE
AMET211NAG: N-ACETYL-D-GLUCOSAMINE
AASP213NAG: N-ACETYL-D-GLUCOSAMINE
ATYR220NAG: N-ACETYL-D-GLUCOSAMINE
AASN222NAG: N-ACETYL-D-GLUCOSAMINE

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UniProtにおけるモチーフ・データベースPROSITEからの機能情報

site_id残基数詳細
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SwissProt/UniProtに記載されている蛋白質分子機能情報

site_id残基数詳細
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CSAにおける酵素触媒機能の情報

site_id残基数詳細

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