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- PDB-2x1w: Crystal Structure of VEGF-C in Complex with Domains 2 and 3 of VEGFR2 -

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基本情報

登録情報
データベース: PDB / ID: 2x1w
タイトルCrystal Structure of VEGF-C in Complex with Domains 2 and 3 of VEGFR2
要素(VASCULAR ENDOTHELIAL GROWTH FACTOR ...) x 2
キーワードHORMONE/SIGNALING PROTEIN / HORMONE-SIGNALING PROTEIN COMPLEX / ANGIOGENESIS / GLYCOPROTEIN / HOST-VIRUS INTERACTION / MEMBRANE / RECEPTOR / LYMPHANGIOGENESIS / IMMUNOGLOBULIN DOMAIN / DEVELOPMENTAL PROTEIN / TRANSMEMBRANE / PHOSPHOPROTEIN / DISULFIDE BOND / MITOGEN
機能・相同性
機能・相同性情報


vascular endothelial growth factor receptor 3 binding / substrate-dependent cell migration / positive regulation of nitric oxide-cGMP mediated signal transduction / positive regulation of lymphangiogenesis / blood vessel endothelial cell differentiation / VEGF ligand-receptor interactions / positive regulation of mast cell chemotaxis / regulation of bone development / cellular response to hydrogen sulfide / morphogenesis of embryonic epithelium ...vascular endothelial growth factor receptor 3 binding / substrate-dependent cell migration / positive regulation of nitric oxide-cGMP mediated signal transduction / positive regulation of lymphangiogenesis / blood vessel endothelial cell differentiation / VEGF ligand-receptor interactions / positive regulation of mast cell chemotaxis / regulation of bone development / cellular response to hydrogen sulfide / morphogenesis of embryonic epithelium / Signaling by membrane-tethered fusions of PDGFRA or PDGFRB / regulation of vascular endothelial growth factor receptor signaling pathway / Neurophilin interactions with VEGF and VEGFR / vascular endothelial growth factor binding / positive regulation of mesenchymal stem cell proliferation / vascular endothelial growth factor receptor-2 signaling pathway / endothelium development / VEGF binds to VEGFR leading to receptor dimerization / endocardium development / vascular wound healing / endothelial cell differentiation / regulation of hematopoietic progenitor cell differentiation / vascular endothelial growth factor receptor activity / post-embryonic camera-type eye morphogenesis / lymph vessel development / mesenchymal cell proliferation / positive regulation of vasculogenesis / induction of positive chemotaxis / positive regulation of BMP signaling pathway / surfactant homeostasis / sprouting angiogenesis / cell migration involved in sprouting angiogenesis / epithelial cell maturation / positive regulation of positive chemotaxis / positive regulation of endothelial cell chemotaxis / positive regulation of cell migration involved in sprouting angiogenesis / anchoring junction / embryonic hemopoiesis / positive regulation of mesenchymal cell proliferation / vascular endothelial growth factor signaling pathway / growth factor binding / lung alveolus development / positive regulation of mitochondrial fission / branching involved in blood vessel morphogenesis / positive regulation of neuroblast proliferation / positive regulation of mitochondrial depolarization / positive regulation of stem cell proliferation / sorting endosome / chemoattractant activity / semaphorin-plexin signaling pathway / regulation of MAPK cascade / positive regulation of cell division / positive regulation of macroautophagy / positive regulation of glial cell proliferation / cellular response to vascular endothelial growth factor stimulus / cell fate commitment / positive regulation of focal adhesion assembly / positive regulation of blood vessel endothelial cell migration / negative regulation of osteoblast differentiation / Integrin cell surface interactions / vascular endothelial growth factor receptor signaling pathway / negative regulation of endothelial cell apoptotic process / glial cell proliferation / vasculogenesis / calcium ion homeostasis / coreceptor activity / ovarian follicle development / negative regulation of blood pressure / positive regulation of endothelial cell proliferation / transmembrane receptor protein tyrosine kinase activity / positive regulation of endothelial cell migration / cell surface receptor protein tyrosine kinase signaling pathway / platelet alpha granule lumen / peptidyl-tyrosine phosphorylation / VEGFR2 mediated cell proliferation / cellular response to leukemia inhibitory factor / animal organ morphogenesis / epithelial cell proliferation / positive regulation of epithelial cell proliferation / stem cell proliferation / positive regulation of protein secretion / growth factor activity / Hsp90 protein binding / receptor protein-tyrosine kinase / VEGFA-VEGFR2 Pathway / integrin binding / positive regulation of protein phosphorylation / positive regulation of angiogenesis / cell junction / cell migration / Platelet degranulation / regulation of cell shape / protein autophosphorylation / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / protein tyrosine kinase activity / angiogenesis / negative regulation of neuron apoptotic process / response to hypoxia / early endosome / positive regulation of ERK1 and ERK2 cascade
類似検索 - 分子機能
CXCXC repeat / CXCXC repeat / Vascular endothelial growth factor receptor 2 (VEGFR2) / VEGFR-2, transmembrane domain / : / : / : / VEGFR-2 Transmembrane domain / Vascular endothelial growth factor receptor 1-like, Ig-like domain / VEGFR1-3, N-terminal Ig-like domain ...CXCXC repeat / CXCXC repeat / Vascular endothelial growth factor receptor 2 (VEGFR2) / VEGFR-2, transmembrane domain / : / : / : / VEGFR-2 Transmembrane domain / Vascular endothelial growth factor receptor 1-like, Ig-like domain / VEGFR1-3, N-terminal Ig-like domain / VEGFR-1-like, immunoglobulin-like domain / PDGF/VEGF domain / Platelet-derived growth factor, conserved site / PDGF/VEGF domain / Platelet-derived growth factor (PDGF) family signature. / Platelet-derived growth factor (PDGF) family profile. / Platelet-derived and vascular endothelial growth factors (PDGF, VEGF) family / Tyrosine-protein kinase, receptor class III, conserved site / Receptor tyrosine kinase class III signature. / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines / Immunoglobulin domain / Cystine-knot cytokine / Immunoglobulin / Immunoglobulin domain / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / : / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Ribbon / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Immunoglobulin subtype / Immunoglobulin / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Immunoglobulins / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
類似検索 - ドメイン・相同性
: / Vascular endothelial growth factor receptor 2 / Vascular endothelial growth factor C
類似検索 - 構成要素
生物種HOMO SAPIENS (ヒト)
手法X線回折 / シンクロトロン / 単一同系置換・異常分散 / 解像度: 2.7 Å
データ登録者Leppanen, V.M. / Prota, A.E. / Jeltsch, M. / Anisimov, A. / Kalkkinen, N. / Strandin, T. / Lankinen, H. / Goldman, A. / Ballmer-Hofer, K. / Alitalo, K.
引用ジャーナル: Proc.Natl.Acad.Sci.USA / 年: 2010
タイトル: Structural Determinants of Growth Factor Binding and Specificity by Vegf Receptor 2.
著者: Leppanen, V.M. / Prota, A.E. / Jeltsch, M. / Anisimov, A. / Kalkkinen, N. / Strandin, T. / Lankinen, H. / Goldman, A. / Ballmer-Hofer, K. / Alitalo, K.
履歴
登録2010年1月8日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02010年3月9日Provider: repository / タイプ: Initial release
改定 1.12012年1月11日Group: Non-polymer description / Version format compliance
改定 2.02020年7月29日Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
カテゴリ: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_chiral / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_chiral.details / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id
解説: Carbohydrate remediation / Provider: repository / タイプ: Remediation
改定 2.12024年10月9日Group: Data collection / Database references / Structure summary
カテゴリ: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: VASCULAR ENDOTHELIAL GROWTH FACTOR C
B: VASCULAR ENDOTHELIAL GROWTH FACTOR C
C: VASCULAR ENDOTHELIAL GROWTH FACTOR C
D: VASCULAR ENDOTHELIAL GROWTH FACTOR C
L: VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 2
M: VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 2
N: VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 2
O: VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 2
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)153,98930
ポリマ－145,1988
非ポリマー8,79122
水3,189177
1
A: VASCULAR ENDOTHELIAL GROWTH FACTOR C
B: VASCULAR ENDOTHELIAL GROWTH FACTOR C
M: VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 2
N: VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 2
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)76,95614
ポリマ－72,5994
非ポリマー4,35710
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area11830 Å2
ΔGint-33.7 kcal/mol
Surface area31640 Å2
手法PISA
2
C: VASCULAR ENDOTHELIAL GROWTH FACTOR C
D: VASCULAR ENDOTHELIAL GROWTH FACTOR C
L: VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 2
O: VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 2
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)77,03316
ポリマ－72,5994
非ポリマー4,43412
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area11970 Å2
ΔGint-19.8 kcal/mol
Surface area31930 Å2
手法PISA
単位格子
Length a, b, c (Å)73.750, 123.830, 211.831
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID
11
21
12
22
13
23
14
24
15
25
16
26

NCSドメイン領域:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 120:142 OR RESSEQ 151:169 OR RESSEQ 172:188 OR RESSEQ 196:213 )
211CHAIN B AND (RESSEQ 120:142 OR RESSEQ 151:169 OR RESSEQ 172:188 OR RESSEQ 196:213 )
112CHAIN C AND (RESSEQ 120:139 OR RESSEQ 141:146 OR RESSEQ...
212CHAIN D AND (RESSEQ 120:139 OR RESSEQ 141:146 OR RESSEQ...
113CHAIN M AND (RESSEQ 134:137 OR RESSEQ 144:201 OR RESSEQ 211:217)
213CHAIN N AND (RESSEQ 134:137 OR RESSEQ 144:201 OR RESSEQ 211:217)
114CHAIN M AND (RESSEQ 221:239 OR RESSEQ 241:264 OR RESSEQ...
214CHAIN N AND (RESSEQ 221:239 OR RESSEQ 241:264 OR RESSEQ...
115CHAIN L AND (RESSEQ 134:137 OR RESSEQ 145:201 OR RESSEQ 209:218)
215CHAIN O AND (RESSEQ 134:137 OR RESSEQ 145:201 OR RESSEQ 209:218)
116CHAIN L AND (RESSEQ 221:261 OR RESSEQ 285:325)
216CHAIN O AND (RESSEQ 221:261 OR RESSEQ 285:325)

NCSアンサンブル:
ID
1
2
3
4
5
6

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要素

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VASCULAR ENDOTHELIAL GROWTH FACTOR ... , 2種, 8分子 ABCDLMNO

#1: タンパク質
VASCULAR ENDOTHELIAL GROWTH FACTOR C / VEGF-C / VASCULAR ENDOTHELIAL GROWTH FACTOR-RELATED PROTEIN / VRP / FLT4 LIGAND / FLT4-L


分子量: 12390.194 Da / 分子数: 4 / 断片: VEGF HOMOLOGY DOMAIN, RESIDUES 112-215 / 変異: YES / 由来タイプ: 組換発現 / 由来: (組換発現) HOMO SAPIENS (ヒト) / プラスミド: PFASTBAC / 細胞株 (発現宿主): SF9
発現宿主: SPODOPTERA FRUGIPERDA (ツマジロクサヨトウ)
参照: UniProt: P49767
#2: タンパク質
VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 2 / VEGF RECEPTOR 2 / VEGFR-2 / KINASE INSERT DOMAIN RECEPTOR / PROTEIN-TYROSINE KINASE RECEPTOR FLK-1 ...VEGF RECEPTOR 2 / VEGFR-2 / KINASE INSERT DOMAIN RECEPTOR / PROTEIN-TYROSINE KINASE RECEPTOR FLK-1 / CD309 / FLK-1


分子量: 23909.270 Da / 分子数: 4 / 断片: IG-LIKE DOMAINS 2 AND 3, RESIDUES 120-326 / 由来タイプ: 組換発現 / 由来: (組換発現) HOMO SAPIENS (ヒト) / プラスミド: PFASTBAC / 細胞株 (発現宿主): SF9
発現宿主: SPODOPTERA FRUGIPERDA (ツマジロクサヨトウ)
参照: UniProt: P35968

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糖 , 3種, 20分子

#3: 多糖
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 586.542 Da / 分子数: 9 / 由来タイプ: 組換発現
記述子タイププログラム
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#4: 多糖
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 424.401 Da / 分子数: 4 / 由来タイプ: 組換発現
記述子タイププログラム
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#6: 糖
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-アセチル-β-D-グルコサミン


タイプ: D-saccharide, beta linking / 分子量: 221.208 Da / 分子数: 7 / 由来タイプ: 組換発現 / 式: C8H15NO6
識別子タイププログラム
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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非ポリマー , 2種, 179分子

#5: 化合物 ChemComp-CS / CESIUM ION / セシウムカチオン


分子量: 132.905 Da / 分子数: 2 / 由来タイプ: 合成 / 式: Cs
#7: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 177 / 由来タイプ: 天然 / 式: H2O

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詳細

構成要素の詳細ENGINEERED RESIDUE IN CHAIN A, CYS 137 TO ALA ENGINEERED RESIDUE IN CHAIN B, CYS 137 TO ALA ...ENGINEERED RESIDUE IN CHAIN A, CYS 137 TO ALA ENGINEERED RESIDUE IN CHAIN B, CYS 137 TO ALA ENGINEERED RESIDUE IN CHAIN C, CYS 137 TO ALA ENGINEERED RESIDUE IN CHAIN D, CYS 137 TO ALA
Has protein modificationY
非ポリマーの詳細NAG, MAN: N-LINKED GLYCANS (NAG AND MAN) HAVE THE SAME CHAIN IDENTIFIER AS THE PROTEIN CHAIN THEY ...NAG, MAN: N-LINKED GLYCANS (NAG AND MAN) HAVE THE SAME CHAIN IDENTIFIER AS THE PROTEIN CHAIN THEY ARE ATTACHED TO.
配列の詳細THE PROTEIN STUDIED COVERS RESIDUES 112-215 WITH A C- TERMINAL 6HIS-TAG AND A C137A MUTATION. THE ...THE PROTEIN STUDIED COVERS RESIDUES 112-215 WITH A C- TERMINAL 6HIS-TAG AND A C137A MUTATION. THE PROTEIN STUDIED COVERS RESIDUES 120-326 WITH THE ARTIFICIAL RESIDUES DPIEGR AT THE C-TERMINUS.

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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: 2.9 Å3/Da / 溶媒含有率: 58 % / 解説: NONE
結晶化pH: 5.2
詳細: 100 MM MES BUFFER, PH 5.0-5.6, 50 MM CSCL AND 28-32 % (W/V) JEFFAMINE 600.

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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: SLS / ビームライン: X06SA / 波長: 1
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2009年5月25日 / 詳細: MIRRORS
放射モノクロメーター: SI(111) MONOCHROMATOR / 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: 1 Å / 相対比: 1
反射解像度: 2.7→53 Å / Num. obs: 53953 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / 冗長度: 6.7 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 20.1
反射 シェル解像度: 2.7→2.8 Å / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 2.8 / % possible all: 99.5

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解析

ソフトウェア
名称バージョン分類
PHENIX(PHENIX.REFINE)精密化
XDSデータ削減
XDSデータスケーリング
SHELXCDE IMPLEMENTED IN HKL2MAP位相決定
精密化構造決定の手法: 単一同系置換・異常分散
開始モデル: NONE

解像度: 2.7→52.958 Å / SU ML: 0.44 / σ(F): 2 / 位相誤差: 28.61 / 立体化学のターゲット値: ML
詳細: RESIDUES A112-A115, B112-B116, B215, C112-C118, D112-D116, M120-M133, M203-M209, M265- -M268, M280- M282, N120-N123, N127-N131, N266-N269, L120- -L122, L129-L132, L205-L207, O120-O122, O128- ...詳細: RESIDUES A112-A115, B112-B116, B215, C112-C118, D112-D116, M120-M133, M203-M209, M265- -M268, M280- M282, N120-N123, N127-N131, N266-N269, L120- -L122, L129-L132, L205-L207, O120-O122, O128-O131, O266- -O268 AND O281 ARE DISORDERED.
Rfactor反射数%反射
Rfree0.2798 2746 5.09 %
Rwork0.2269 --
obs0.2297 53953 99.61 %
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 / Bsol: 44.118 Å2 / ksol: 0.313 e/Å3
原子変位パラメータ
Baniso -1Baniso -2Baniso -3
1-1.4363 Å20 Å20 Å2
2--5.1571 Å20 Å2
3----6.5934 Å2
精密化ステップサイクル: LAST / 解像度: 2.7→52.958 Å
タンパク質核酸リガンド溶媒全体
原子数8980 0 563 177 9720
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0059778
X-RAY DIFFRACTIONf_angle_d1.00413229
X-RAY DIFFRACTIONf_dihedral_angle_d25.3173725
X-RAY DIFFRACTIONf_chiral_restr0.0621612
X-RAY DIFFRACTIONf_plane_restr0.0031579
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDタイプRms dev position (Å)
11A600X-RAY DIFFRACTIONPOSITIONAL
12B600X-RAY DIFFRACTIONPOSITIONAL0.035
21C631X-RAY DIFFRACTIONPOSITIONAL
22D631X-RAY DIFFRACTIONPOSITIONAL0.046
31M539X-RAY DIFFRACTIONPOSITIONAL
32N539X-RAY DIFFRACTIONPOSITIONAL0.024
41M720X-RAY DIFFRACTIONPOSITIONAL
42N720X-RAY DIFFRACTIONPOSITIONAL0.041
51L558X-RAY DIFFRACTIONPOSITIONAL
52O558X-RAY DIFFRACTIONPOSITIONAL0.03
61L639X-RAY DIFFRACTIONPOSITIONAL
62O639X-RAY DIFFRACTIONPOSITIONAL0.037
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.74660.37791550.30652500X-RAY DIFFRACTION99
2.7466-2.79650.33191480.28012483X-RAY DIFFRACTION100
2.7965-2.85030.33321130.27322565X-RAY DIFFRACTION100
2.8503-2.90850.30761310.26412521X-RAY DIFFRACTION99
2.9085-2.97170.31231270.26942540X-RAY DIFFRACTION100
2.9717-3.04080.35021490.27172506X-RAY DIFFRACTION100
3.0408-3.11690.34761400.27052544X-RAY DIFFRACTION100
3.1169-3.20110.31571480.26012549X-RAY DIFFRACTION100
3.2011-3.29530.32821340.252506X-RAY DIFFRACTION100
3.2953-3.40170.31011270.2382565X-RAY DIFFRACTION100
3.4017-3.52320.29651580.23042540X-RAY DIFFRACTION100
3.5232-3.66420.24981270.21742544X-RAY DIFFRACTION100
3.6642-3.8310.28111040.21042577X-RAY DIFFRACTION100
3.831-4.03290.25521600.20182544X-RAY DIFFRACTION100
4.0329-4.28540.2531390.18232555X-RAY DIFFRACTION100
4.2854-4.61610.23351460.17072588X-RAY DIFFRACTION100
4.6161-5.08040.1971190.16512587X-RAY DIFFRACTION100
5.0804-5.81470.23871400.18522607X-RAY DIFFRACTION100
5.8147-7.32280.24771430.20952640X-RAY DIFFRACTION99
7.3228-52.96790.28871380.25882746X-RAY DIFFRACTION99
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)
10.8401-0.01131.08451.9836-1.55663.59920.0041-0.2489-0.08710.0777-0.3019-0.2526-0.6301-0.28170.26630.5038-0.02940.00650.32790.13250.3587-6.6294-9.465910.8369
26.2004-5.37420.87795.4063-1.23462.08380.05611.00680.40260.0106-0.6136-0.136-0.0292-0.17150.46010.41510.00390.0480.3713-0.00720.3839-27.44361.8417-3.3131
33.8177-5.18741.12058.1226-0.73871.4587-0.32590.3878-1.44890.39110.22652.13080.0729-0.57680.06790.11610.08090.02120.3603-0.04820.4499-34.5321.3699-2.2784
41.20750.0247-0.09520.0114-0.31132.0097-0.0044-0.55870.0750.3759-0.34350.05490.80950.01070.16910.626-0.0021-0.01590.2732-0.02920.5446-33.621712.44187.9237
5-0.0712-0.1094-0.14850.27420.39121.6568-0.09380.15860.1891-0.4352-0.0535-0.2-0.58270.1253-0.23050.4016-0.0580.04820.1280.15790.3242-11.28961.1811-1.5343
60.5777-0.28460.63581.9089-0.46171.0022-0.12780.5170.57850.2174-0.209-1.0172-0.09190.48510.26950.37-0.12120.01190.49440.13280.5916-4.63842.26310.4008
75.00890.53730.52518.2117-5.30743.5247-0.3505-1.2747-0.05221.3401-0.43530.214-0.87590.37620.47440.4393-0.08370.0880.32760.03650.1738-30.1003-17.668763.3013
80.9781.6669-1.21183.9043-2.49361.5445-0.36940.06270.0841-0.6908-0.0018-0.110.32520.03140.34270.1804-0.0398-0.02610.266-0.09280.2926-25.26345.164154.071
92.24820.60640.93621.311-0.32510.5445-0.0003-0.19510.4041-0.03960.00330.43630.0308-0.04150.0170.1228-0.01170.01610.1856-0.10160.2486-27.994810.710556.0724
102.4317-0.29790.82451.49450.85761.4615-0.2695-1.31260.06830.7347-0.2613-0.1233-0.2223-0.53730.03640.27650.0359-0.20780.5484-0.08870.2371-15.849211.148866.273
110.61830.18-0.23341.4649-0.1120.2028-0.15390.0755-0.1659-0.2979-0.0282-0.1080.0962-0.18040.12810.251-0.05250.01680.3389-0.1090.2421-22.0036-10.442652.0047
122.6148-0.30140.44190.85290.17123.25510.27050.1777-1.1310.33310.0562-0.59940.89540.1198-0.31780.31630.07630.00160.2499-0.15970.5809-18.9689-16.382952.2172
130.3340.5564-0.62580.8416-0.74471.15670.3603-0.0151-0.20040.5235-0.2364-0.111-0.13260.0179-0.07440.5259-0.15740.1060.3368-0.11650.4096-48.0187-23.259763.2995
141.3507-0.7668-0.92111.57741.57945.05460.1839-0.0002-0.0172-0.3185-0.29690.0579-0.5624-0.52040.10630.3361-0.063-0.0210.1836-0.02980.1662-34.3956-22.581225.1451
152.1654-0.49450.94580.71720.7261.1363-0.7007-0.29210.42970.16620.46940.066-1.3642-0.16880.31341.18630.3022-0.29740.48510.04430.517-31.394731.63554.4263
161.4209-0.2725-0.19521.88150.50562.1871-0.32850.324-0.1109-0.18650.06480.3704-0.5011-0.37810.14710.16210.1665-0.05960.37730.02620.2448-37.317311.7693-30.1049
173.9703-1.20550.90881.5964-2.10622.79050.1186-0.2184-0.4079-0.0602-0.0498-0.04040.91070.1686-0.04140.62990.09250.13110.33310.15440.3508-8.5247-28.15399.7103
180.99940.55440.97171.9367-0.74541.7509-0.23220.31470.34160.24640.1989-0.1671-0.10890.25710.00540.11580.08940.05570.21580.06590.19451.6071-13.9217-28.2411
190.3625-0.2921-0.24821.3624-0.29442.6723-0.0312-0.39790.33440.1454-0.138-0.6524-0.23680.9372-0.00140.1257-0.1764-0.14240.52310.01260.53272.332214.446265.6796
200.8563-0.02130.69553.114-1.38024.4260.03980.22820.07-0.4512-0.2756-0.2168-0.26790.82620.17560.3810.01440.08990.30080.04570.3836-9.020622.100326.3328
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 116:130)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 131:170)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 171:213)
4X-RAY DIFFRACTION4(CHAIN B AND RESID 117:130)
5X-RAY DIFFRACTION5(CHAIN B AND RESID 131:170)
6X-RAY DIFFRACTION6(CHAIN B AND RESID 171:214)
7X-RAY DIFFRACTION7(CHAIN C AND RESID 119:130)
8X-RAY DIFFRACTION8(CHAIN C AND RESID 131:170)
9X-RAY DIFFRACTION9(CHAIN C AND RESID 171:215)
10X-RAY DIFFRACTION10(CHAIN D AND RESID 117:130)
11X-RAY DIFFRACTION11(CHAIN D AND RESID 131:170)
12X-RAY DIFFRACTION12(CHAIN D AND RESID 171:215)
13X-RAY DIFFRACTION13(CHAIN L AND RESID 123:219)
14X-RAY DIFFRACTION14(CHAIN L AND RESID 220:326)
15X-RAY DIFFRACTION15(CHAIN M AND RESID 133:219)
16X-RAY DIFFRACTION16(CHAIN M AND RESID 220:326)
17X-RAY DIFFRACTION17(CHAIN N AND RESID 124:219)
18X-RAY DIFFRACTION18(CHAIN N AND RESID 220:326)
19X-RAY DIFFRACTION19(CHAIN O AND RESID 123:219)
20X-RAY DIFFRACTION20(CHAIN O AND RESID 220:325)

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万見について

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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

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