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- PDB-6qxp: Protein peptide complex -

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IDまたはキーワード:

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基本情報

登録情報
データベース: PDB / ID: 6qxp
タイトルProtein peptide complex
要素
  • Leucine-rich repeat extensin-like protein 2
  • Protein RALF-like 4
キーワードPLANT PROTEIN / Leucine rich extensin / peptide signaling / cell wall signaling / LRR
機能・相同性
機能・相同性情報


regulation of pollen tube growth / apoplast / calcium-mediated signaling / cell wall organization / hormone activity / cell-cell signaling / extracellular region
類似検索 - 分子機能
: / Rapid ALkalinization Factor / Rapid ALkalinization Factor (RALF) / Leucine-rich repeat-containing N-terminal, plant-type / Leucine rich repeat N-terminal domain / Leucine Rich Repeat / Leucine rich repeat / Leucine-rich repeat / Leucine-rich repeat domain superfamily
類似検索 - ドメイン・相同性
Leucine-rich repeat extensin-like protein 2 / Protein RALF-like 4
類似検索 - 構成要素
生物種Arabidopsis (植物)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.201 Å
データ登録者Moussu, S. / Caroline, C. / Santos-Fernandez, G. / Wehrle, S. / Grossniklaus, U. / Santiago, J.
資金援助 スイス, 1件
組織認可番号国
European Research Council716358 スイス
引用ジャーナル: Proc.Natl.Acad.Sci.USA / 年: 2020
タイトル: Structural basis for recognition of RALF peptides by LRX proteins during pollen tube growth.
著者: Moussu, S. / Broyart, C. / Santos-Fernandez, G. / Augustin, S. / Wehrle, S. / Grossniklaus, U. / Santiago, J.
履歴
登録2019年3月7日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02020年3月25日Provider: repository / タイプ: Initial release
改定 1.12020年4月8日Group: Database references / カテゴリ: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
改定 2.02020年7月29日Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
カテゴリ: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / 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 / 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.type_symbol / _chem_comp.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
解説: Carbohydrate remediation / Provider: repository / タイプ: Remediation

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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: Leucine-rich repeat extensin-like protein 2
B: Leucine-rich repeat extensin-like protein 2
C: Leucine-rich repeat extensin-like protein 2
D: Leucine-rich repeat extensin-like protein 2
E: Leucine-rich repeat extensin-like protein 2
F: Leucine-rich repeat extensin-like protein 2
G: Leucine-rich repeat extensin-like protein 2
H: Leucine-rich repeat extensin-like protein 2
I: Protein RALF-like 4
J: Protein RALF-like 4
K: Protein RALF-like 4
L: Protein RALF-like 4
M: Protein RALF-like 4
N: Protein RALF-like 4
O: Protein RALF-like 4
P: Protein RALF-like 4
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)383,37045
ポリマ－371,59616
非ポリマー11,77429
水00
1
A: Leucine-rich repeat extensin-like protein 2
I: Protein RALF-like 4
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)48,2867
ポリマ－46,4502
非ポリマー1,8375
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
2
B: Leucine-rich repeat extensin-like protein 2
J: Protein RALF-like 4
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)47,1983
ポリマ－46,4502
非ポリマー7491
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
3
C: Leucine-rich repeat extensin-like protein 2
K: Protein RALF-like 4
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)48,4716
ポリマ－46,4502
非ポリマー2,0224
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
4
D: Leucine-rich repeat extensin-like protein 2
L: Protein RALF-like 4
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)47,9036
ポリマ－46,4502
非ポリマー1,4534
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
5
E: Leucine-rich repeat extensin-like protein 2
M: Protein RALF-like 4
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)48,4487
ポリマ－46,4502
非ポリマー1,9995
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
6
F: Leucine-rich repeat extensin-like protein 2
N: Protein RALF-like 4
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)47,6415
ポリマ－46,4502
非ポリマー1,1913
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
7
G: Leucine-rich repeat extensin-like protein 2
O: Protein RALF-like 4
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)48,1657
ポリマ－46,4502
非ポリマー1,7165
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
8
H: Leucine-rich repeat extensin-like protein 2
P: Protein RALF-like 4
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)47,2574
ポリマ－46,4502
非ポリマー8082
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)119.988, 119.988, 305.736
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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要素

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タンパク質 , 2種, 16分子 ABCDEFGHIJKLMNOP

#1: タンパク質
Leucine-rich repeat extensin-like protein 2 / LRR/EXTENSIN2 / Cell wall hydroxyproline-rich glycoprotein


分子量: 39631.609 Da / 分子数: 8 / 由来タイプ: 組換発現 / 由来: (組換発現) Arabidopsis (植物) / 組織: pollen / Cell: pollen / 遺伝子: LRX2, At1g62440, F24O1.18, T3P18.1 / 器官: pollen / プラスミド: pfastBAc / 細胞株 (発現宿主): TNAO38 / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: O48809
#2: タンパク質
Protein RALF-like 4


分子量: 6817.940 Da / 分子数: 8 / 由来タイプ: 組換発現 / 由来: (組換発現) Arabidopsis (植物) / 組織: pollen / Cell: pollen / 遺伝子: RALFL4, At1g28270, F3H9.8 / 器官: pollen / プラスミド: pfastBAc / 細胞株 (発現宿主): TNAO38 / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: Q9FZA0

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糖 , 5種, 29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: 7 / 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 alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-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: 748.682 Da / 分子数: 1 / 由来タイプ: 組換発現
記述子タイププログラム
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#5: 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: 6 / 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: 多糖 alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-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: 748.682 Da / 分子数: 2 / 由来タイプ: 組換発現
記述子タイププログラム
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#7: 糖
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / 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: 13 / 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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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: 3.06 Å3/Da / 溶媒含有率: 59.76 %
結晶化温度: 292 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 5 / 詳細: 0.1 Bis-tris pH5 , 0.2 sodium acetate, 20% PEG 3350

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データ収集

回折平均測定温度: 80 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: SLS / ビームライン: X06DA / 波長: 1.00003 Å
検出器タイプ: DECTRIS PILATUS 2M-F / 検出器: PIXEL / 日付: 2018年5月13日
放射モノクロメーター: Fixed-exit LN2 cooled double / 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: 1.00003 Å / 相対比: 1
反射解像度: 3.201→59.99 Å / Num. obs: 45468 / % possible obs: 99.82 % / Observed criterion σ(I): 1.2 / 冗長度: 20.7 % / Biso Wilson estimate: 78.5 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.416 / Rrim(I) all: 0.42 / Net I/σ(I): 10.82
反射 シェル解像度: 3.201→3.315 Å / 冗長度: 25.9 % / Mean I/σ(I) obs: 1.43 / Num. unique obs: 7103 / CC1/2: 0.58 / Rrim(I) all: 2.8 / Rsym value: 2.9 / % possible all: 99.82

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解析

ソフトウェア
名称バージョン分類
PHENIXv1.14精密化
XDS2018データ削減
XSCALE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 / 解像度: 3.201→59.99 Å / SU ML: 0.56 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 31.1
Rfactor反射数%反射
Rfree0.2741 7061 5.04 %
Rwork0.2274 --
obs0.2298 140169 99.68 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
精密化ステップサイクル: LAST / 解像度: 3.201→59.99 Å
タンパク質核酸リガンド溶媒全体
原子数23520 0 773 0 24293
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00324927
X-RAY DIFFRACTIONf_angle_d0.74533923
X-RAY DIFFRACTIONf_dihedral_angle_d8.58814853
X-RAY DIFFRACTIONf_chiral_restr0.053867
X-RAY DIFFRACTIONf_plane_restr0.0054404
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2006-3.2370.41152810.37054194X-RAY DIFFRACTION94
3.237-3.2750.41522000.3764422X-RAY DIFFRACTION100
3.275-3.3150.42722140.36694513X-RAY DIFFRACTION100
3.315-3.35690.36342360.33264428X-RAY DIFFRACTION100
3.3569-3.40110.37971970.33044473X-RAY DIFFRACTION100
3.4011-3.44770.36182360.32234458X-RAY DIFFRACTION100
3.4477-3.49690.3272430.32084435X-RAY DIFFRACTION100
3.4969-3.54910.39762040.31414470X-RAY DIFFRACTION100
3.5491-3.60460.32172080.30644515X-RAY DIFFRACTION100
3.6046-3.66370.36572060.29914480X-RAY DIFFRACTION100
3.6637-3.72680.29062600.26724431X-RAY DIFFRACTION100
3.7268-3.79460.30672760.24534339X-RAY DIFFRACTION100
3.7946-3.86760.26772280.2324554X-RAY DIFFRACTION100
3.8676-3.94650.2542160.2264423X-RAY DIFFRACTION100
3.9465-4.03230.31132480.21024389X-RAY DIFFRACTION100
4.0323-4.12610.27242280.21014527X-RAY DIFFRACTION100
4.1261-4.22920.21791960.18984433X-RAY DIFFRACTION100
4.2292-4.34350.2382640.1844454X-RAY DIFFRACTION100
4.3435-4.47130.25322440.18534488X-RAY DIFFRACTION100
4.4713-4.61560.27442700.1824412X-RAY DIFFRACTION100
4.6156-4.78050.232040.17974435X-RAY DIFFRACTION100
4.7805-4.97180.25352280.18054489X-RAY DIFFRACTION100
4.9718-5.19790.24682060.18784447X-RAY DIFFRACTION100
5.1979-5.47180.23342520.19594477X-RAY DIFFRACTION100
5.4718-5.81440.29682100.22764418X-RAY DIFFRACTION100
5.8144-6.26290.26632380.21924472X-RAY DIFFRACTION100
6.2629-6.89230.28382160.20874431X-RAY DIFFRACTION100
6.8923-7.88770.24383080.20274392X-RAY DIFFRACTION100
7.8877-9.93040.23162840.2084431X-RAY DIFFRACTION100
9.9304-60.00450.23022600.20944278X-RAY DIFFRACTION97
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)
10.0115-0.01740.00270.0275-0.00320.0487-0.0067-0.0667-0.0931-0.0135-0.32920.0950.1745-0.0966-0.00061.0497-0.1179-0.21080.451-0.00210.83456.58046.67059.8255
20.20440.117-0.07740.18090.13270.335-0.0647-0.0436-0.18090.0928-0.22460.35840.2032-0.0589-0.32970.8961-0.0927-0.08050.2202-0.00530.643763.587515.74195.6082
30.03230.0029-0.00290.0002-0.00350.01470.0173-0.0041-0.08050.072-0.06270.14270.0001-0.01780.00320.76370.1126-0.22910.2928-0.06950.487569.000323.4181-3.7428
40.0641-0.0538-0.04660.0890.03840.0750.1190.0918-0.0165-0.2214-0.00970.0680.1774-0.0350.3560.85580.22-0.3223-0.0824-0.14930.420878.481829.24-8.4808
50.1415-0.0982-0.03280.09140.05490.0389-0.0412-0.1045-0.02420.00270.0336-0.18660.06750.0318-0.15030.57090.2203-0.06560.2402-0.13030.400395.356633.9259-7.0196
60.12720.03730.11760.02710.06290.158-0.0149-0.1321-0.2111-0.22960.03870.0280.06520.02640.07210.84580.3720.00950.7821-0.26850.7722106.746927.6633-8.1835
70.2469-0.18410.23010.6918-0.37630.2938-0.3614-0.0470.2106-0.2949-0.23970.06020.00680.0786-0.17180.8050.2071-0.02160.5348-0.04260.538397.715634.8114-21.2639
80.0228-0.0629-0.01680.17480.04750.01340.00010.0466-0.0067-0.0942-0.05230.03520.0201-0.1588-0.00840.9872-0.0095-0.41650.8348-0.3950.880147.92527.0917-26.6887
90.21710.14440.0690.13380.13520.2547-0.03230.0782-0.03920.0381-0.18020.08850.0291-0.122-0.1791.0526-0.0312-0.34940.3453-0.22940.830258.7492.9216-26.7698
100.00750.0145-0.02550.0263-0.04770.0899-0.05640.0311-0.160.0955-0.16120.13270.1124-0.142-0.17381.2317-0.0586-0.35170.411-0.24960.989863.0195-6.6196-16.3419
110.00280.01690.0130.08590.05550.0365-0.04010.0418-0.03230.0416-0.01010.1007-0.0040.00470.01611.6263-0.0974-0.29810.3368-0.11061.126971.9333-16.2357-10.74
120.01390.01270.01790.03010.06610.1659-0.06620.0383-0.1-0.07940.04820.02120.10630.03710.01271.76540.178-0.39070.4811-0.14541.333884.3152-24.3249-15.0622
130.00580.00120.010.0202-0.00030.0111-0.01770.02160.0211-0.04050.0687-0.0348-0.01220.0808-01.94370.2468-0.31221.0174-0.34731.662994.605-26.6186-18.4231
140.0133-0.0108-0.00430.00340.00360.0007-0.00210.07230.00090.1349-0.045-0.0804-0.0207-0.0386-0.00011.36290.3463-0.25521.5336-0.32211.2991102.4375-20.931-12.9616
150.00410.00110.00180.00520.0004-0.001-0.02110.01060.00880.0404-0.0081-0.03790.0785-0.049-01.44840.20420.03411.05190.05931.578188.6499-28.30170.4564
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精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 44 through 82 )
2X-RAY DIFFRACTION2chain 'A' and (resid 83 through 161 )
3X-RAY DIFFRACTION3chain 'A' and (resid 162 through 183 )
4X-RAY DIFFRACTION4chain 'A' and (resid 184 through 256 )
5X-RAY DIFFRACTION5chain 'A' and (resid 257 through 319 )
6X-RAY DIFFRACTION6chain 'A' and (resid 320 through 356 )
7X-RAY DIFFRACTION7chain 'A' and (resid 357 through 388 )
8X-RAY DIFFRACTION8chain 'B' and (resid 42 through 66 )
9X-RAY DIFFRACTION9chain 'B' and (resid 67 through 135 )
10X-RAY DIFFRACTION10chain 'B' and (resid 136 through 183 )
11X-RAY DIFFRACTION11chain 'B' and (resid 184 through 236 )
12X-RAY DIFFRACTION12chain 'B' and (resid 237 through 302 )
13X-RAY DIFFRACTION13chain 'B' and (resid 303 through 322 )
14X-RAY DIFFRACTION14chain 'B' and (resid 323 through 365 )
15X-RAY DIFFRACTION15chain 'B' and (resid 366 through 381 )
16X-RAY DIFFRACTION16chain 'C' and (resid 40 through 82 )
17X-RAY DIFFRACTION17chain 'C' and (resid 83 through 113 )
18X-RAY DIFFRACTION18chain 'C' and (resid 114 through 183 )
19X-RAY DIFFRACTION19chain 'C' and (resid 184 through 250 )
20X-RAY DIFFRACTION20chain 'C' and (resid 251 through 302 )
21X-RAY DIFFRACTION21chain 'C' and (resid 303 through 341 )
22X-RAY DIFFRACTION22chain 'C' and (resid 342 through 361 )
23X-RAY DIFFRACTION23chain 'C' and (resid 362 through 386 )
24X-RAY DIFFRACTION24chain 'D' and (resid 42 through 82 )
25X-RAY DIFFRACTION25chain 'D' and (resid 83 through 135 )
26X-RAY DIFFRACTION26chain 'D' and (resid 136 through 250 )
27X-RAY DIFFRACTION27chain 'D' and (resid 251 through 298 )
28X-RAY DIFFRACTION28chain 'D' and (resid 299 through 319 )
29X-RAY DIFFRACTION29chain 'D' and (resid 320 through 337 )
30X-RAY DIFFRACTION30chain 'D' and (resid 338 through 362 )
31X-RAY DIFFRACTION31chain 'D' and (resid 363 through 382 )
32X-RAY DIFFRACTION32chain 'E' and (resid 41 through 82 )
33X-RAY DIFFRACTION33chain 'E' and (resid 83 through 183 )
34X-RAY DIFFRACTION34chain 'E' and (resid 184 through 250 )
35X-RAY DIFFRACTION35chain 'E' and (resid 251 through 274 )
36X-RAY DIFFRACTION36chain 'E' and (resid 275 through 302 )
37X-RAY DIFFRACTION37chain 'E' and (resid 303 through 322 )
38X-RAY DIFFRACTION38chain 'E' and (resid 323 through 356 )
39X-RAY DIFFRACTION39chain 'E' and (resid 357 through 386 )
40X-RAY DIFFRACTION40chain 'F' and (resid 42 through 66 )
41X-RAY DIFFRACTION41chain 'F' and (resid 67 through 131 )
42X-RAY DIFFRACTION42chain 'F' and (resid 132 through 155 )
43X-RAY DIFFRACTION43chain 'F' and (resid 156 through 183 )
44X-RAY DIFFRACTION44chain 'F' and (resid 184 through 250 )
45X-RAY DIFFRACTION45chain 'F' and (resid 251 through 302 )
46X-RAY DIFFRACTION46chain 'F' and (resid 303 through 319 )
47X-RAY DIFFRACTION47chain 'F' and (resid 320 through 346 )
48X-RAY DIFFRACTION48chain 'F' and (resid 347 through 367 )
49X-RAY DIFFRACTION49chain 'F' and (resid 368 through 387 )
50X-RAY DIFFRACTION50chain 'G' and (resid 44 through 82 )
51X-RAY DIFFRACTION51chain 'G' and (resid 83 through 113 )
52X-RAY DIFFRACTION52chain 'G' and (resid 114 through 161 )
53X-RAY DIFFRACTION53chain 'G' and (resid 162 through 183 )
54X-RAY DIFFRACTION54chain 'G' and (resid 184 through 250 )
55X-RAY DIFFRACTION55chain 'G' and (resid 251 through 319 )
56X-RAY DIFFRACTION56chain 'G' and (resid 320 through 356 )
57X-RAY DIFFRACTION57chain 'G' and (resid 357 through 388 )
58X-RAY DIFFRACTION58chain 'H' and (resid 43 through 82 )
59X-RAY DIFFRACTION59chain 'H' and (resid 83 through 135 )
60X-RAY DIFFRACTION60chain 'H' and (resid 136 through 161 )
61X-RAY DIFFRACTION61chain 'H' and (resid 162 through 225 )
62X-RAY DIFFRACTION62chain 'H' and (resid 226 through 298 )
63X-RAY DIFFRACTION63chain 'H' and (resid 299 through 327 )
64X-RAY DIFFRACTION64chain 'H' and (resid 328 through 358 )
65X-RAY DIFFRACTION65chain 'H' and (resid 359 through 378 )
66X-RAY DIFFRACTION66chain 'I' and (resid 1061 through 1082 )
67X-RAY DIFFRACTION67chain 'I' and (resid 1083 through 1095 )
68X-RAY DIFFRACTION68chain 'I' and (resid 1096 through 1107 )
69X-RAY DIFFRACTION69chain 'J' and (resid 1061 through 1079 )
70X-RAY DIFFRACTION70chain 'J' and (resid 1080 through 1084 )
71X-RAY DIFFRACTION71chain 'J' and (resid 1085 through 1089 )
72X-RAY DIFFRACTION72chain 'J' and (resid 1090 through 1106 )
73X-RAY DIFFRACTION73chain 'K' and (resid 1062 through 1079 )
74X-RAY DIFFRACTION74chain 'K' and (resid 1080 through 1084 )
75X-RAY DIFFRACTION75chain 'K' and (resid 1085 through 1089 )
76X-RAY DIFFRACTION76chain 'K' and (resid 1090 through 1094 )
77X-RAY DIFFRACTION77chain 'K' and (resid 1095 through 1099 )
78X-RAY DIFFRACTION78chain 'K' and (resid 1100 through 1106 )
79X-RAY DIFFRACTION79chain 'L' and (resid 1061 through 1069 )
80X-RAY DIFFRACTION80chain 'L' and (resid 1070 through 1079 )
81X-RAY DIFFRACTION81chain 'L' and (resid 1080 through 1084 )
82X-RAY DIFFRACTION82chain 'L' and (resid 1085 through 1094 )
83X-RAY DIFFRACTION83chain 'L' and (resid 1095 through 1099 )
84X-RAY DIFFRACTION84chain 'L' and (resid 1100 through 1107 )
85X-RAY DIFFRACTION85chain 'M' and (resid 1061 through 1069 )
86X-RAY DIFFRACTION86chain 'M' and (resid 1070 through 1084 )
87X-RAY DIFFRACTION87chain 'M' and (resid 1085 through 1089 )
88X-RAY DIFFRACTION88chain 'M' and (resid 1090 through 1107 )
89X-RAY DIFFRACTION89chain 'N' and (resid 1062 through 1069 )
90X-RAY DIFFRACTION90chain 'N' and (resid 1070 through 1084 )
91X-RAY DIFFRACTION91chain 'N' and (resid 1085 through 1094 )
92X-RAY DIFFRACTION92chain 'N' and (resid 1095 through 1099 )
93X-RAY DIFFRACTION93chain 'N' and (resid 1100 through 1107 )
94X-RAY DIFFRACTION94chain 'O' and (resid 1061 through 1074 )
95X-RAY DIFFRACTION95chain 'O' and (resid 1075 through 1084 )
96X-RAY DIFFRACTION96chain 'O' and (resid 1085 through 1094 )
97X-RAY DIFFRACTION97chain 'O' and (resid 1095 through 1107 )
98X-RAY DIFFRACTION98chain 'P' and (resid 1062 through 1069 )
99X-RAY DIFFRACTION99chain 'P' and (resid 1070 through 1079 )
100X-RAY DIFFRACTION100chain 'P' and (resid 1080 through 1089 )
101X-RAY DIFFRACTION101chain 'P' and (resid 1090 through 1094 )
102X-RAY DIFFRACTION102chain 'P' and (resid 1095 through 1099 )
103X-RAY DIFFRACTION103chain 'P' and (resid 1100 through 1106 )

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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