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- PDB-4v98: The 8S snRNP Assembly Intermediate -

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基本情報

登録情報
データベース: PDB / ID: 4v98
タイトルThe 8S snRNP Assembly Intermediate
要素
  • (Small nuclear ribonucleoprotein ...) x 5
  • CG10419
  • Icln
  • LD23602p
キーワードSPLICING / Complex / Assembly Machinery
機能・相同性
機能・相同性情報


SmD-containing SMN-Sm protein complex / oocyte morphogenesis / cytoplasmic U snRNP body assembly / flight behavior / larval development / lumen formation, open tracheal system / cytoplasmic U snRNP body / SMN-Gemin2 complex / larval locomotory behavior / basal protein localization ...SmD-containing SMN-Sm protein complex / oocyte morphogenesis / cytoplasmic U snRNP body assembly / flight behavior / larval development / lumen formation, open tracheal system / cytoplasmic U snRNP body / SMN-Gemin2 complex / larval locomotory behavior / basal protein localization / terminal button organization / Gemini of coiled bodies / SMN complex / positive regulation of synaptic assembly at neuromuscular junction / positive regulation of synaptic transmission, cholinergic / neuromuscular synaptic transmission / U7 snRNP / stem cell division / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / AMPA glutamate receptor clustering / U12-type spliceosomal complex / methylosome / 7-methylguanosine cap hypermethylation / pICln-Sm protein complex / P-body assembly / small nuclear ribonucleoprotein complex / SMN-Sm protein complex / spliceosomal tri-snRNP complex / telomerase holoenzyme complex / cell volume homeostasis / P granule / U2-type spliceosomal complex / U2-type precatalytic spliceosome / I band / mRNA cis splicing, via spliceosome / commitment complex / U2-type prespliceosome assembly / U2-type catalytic step 2 spliceosome / embryo development ending in birth or egg hatching / U4 snRNP / chloride transport / U2 snRNP / RNA Polymerase II Transcription Termination / U1 snRNP / U2-type prespliceosome / precatalytic spliceosome / neuromuscular junction development / mRNA Splicing - Minor Pathway / spliceosomal complex assembly / alpha-actinin binding / chromosome organization / U5 snRNP / protein-RNA complex assembly / spliceosomal snRNP assembly / Cajal body / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / adult locomotory behavior / excitatory postsynaptic potential / stem cell proliferation / central nervous system development / stem cell differentiation / spliceosomal complex / neuromuscular junction / Z disc / mRNA splicing, via spliceosome / snRNP Assembly / SARS-CoV-2 modulates host translation machinery / postsynapse / cytoskeleton / RNA binding / extracellular exosome / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
類似検索 - 分子機能
ICln / Protein ICln/Lot5/Saf5 / Regulator of volume decrease after cellular swelling / Gem-associated protein 2 / Gemin2/Brr1 / Survival motor neuron (SMN) interacting protein 1 (SIP1) / : / : / Survival Motor Neuron, YG-box / Survival Motor Neuron, Gemin2-binding domain ...ICln / Protein ICln/Lot5/Saf5 / Regulator of volume decrease after cellular swelling / Gem-associated protein 2 / Gemin2/Brr1 / Survival motor neuron (SMN) interacting protein 1 (SIP1) / : / : / Survival Motor Neuron, YG-box / Survival Motor Neuron, Gemin2-binding domain / SMN complex subunit Smn1 / : / Survival motor neuron, Tudor domain / Survival motor neuron protein (SMN), Tudor domain / Small nuclear ribonucleoprotein D1 / Small nuclear ribonucleoprotein Sm D2 / Small nuclear ribonucleoprotein E / Small nuclear ribonucleoprotein G / Small nuclear ribonucleoprotein F / Tudor domain / Tudor domain / Like-Sm (LSM) domain containing protein, LSm4/SmD1/SmD3 / Sm-like protein Lsm7/SmG / Sm-like protein Lsm6/SmF / LSM domain / LSM domain, eukaryotic/archaea-type / snRNP Sm proteins / : / Sm domain profile. / LSM domain superfamily / PH-like domain superfamily
類似検索 - ドメイン・相同性
Methylosome subunit pICln / Small nuclear ribonucleoprotein E / Small nuclear ribonucleoprotein F / Small nuclear ribonucleoprotein G / Small nuclear ribonucleoprotein Sm D1 / Small nuclear ribonucleoprotein Sm D2 / Methylosome subunit pICln / Survival motor neuron protein / Gem-associated protein 2
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
Drosophila melanogaster (キイロショウジョウバエ)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.1 Å
データ登録者Grimm, C. / Pelz, J.P. / Schindelin, H. / Diederichs, K. / Kuper, J. / Kisker, C.
引用ジャーナル: Mol Cell / 年: 2013
タイトル: Structural basis of assembly chaperone- mediated snRNP formation.
著者: Clemens Grimm / Ashwin Chari / Jann-Patrick Pelz / Jochen Kuper / Caroline Kisker / Kay Diederichs / Holger Stark / Hermann Schindelin / Utz Fischer /
要旨: Small nuclear ribonucleoproteins (snRNPs) represent key constituents of major and minor spliceosomes. snRNPs contain a common core, composed of seven Sm proteins bound to snRNA, which forms in a step- ...Small nuclear ribonucleoproteins (snRNPs) represent key constituents of major and minor spliceosomes. snRNPs contain a common core, composed of seven Sm proteins bound to snRNA, which forms in a step-wise and factor-mediated reaction. The assembly chaperone pICln initially mediates the formation of an otherwise unstable pentameric Sm protein unit. This so-called 6S complex docks subsequently onto the SMN complex, which removes pICln and enables the transfer of pre-assembled Sm proteins onto snRNA. X-ray crystallography and electron microscopy was used to investigate the structural basis of snRNP assembly. The 6S complex structure identifies pICln as an Sm protein mimic, which enables the topological organization of the Sm pentamer in a closed ring. A second structure of 6S bound to the SMN complex components SMN and Gemin2 uncovers a plausible mechanism of pICln elimination and Sm protein activation for snRNA binding. Our studies reveal how assembly factors facilitate formation of RNA-protein complexes in vivo.
履歴
登録2012年5月15日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02014年7月9日Provider: repository / タイプ: Initial release
置き換え2014年12月10日ID: 4F77, 1VU2, 1VU3
改定 1.12014年12月10日Group: Other
改定 1.22023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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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
AI: Small nuclear ribonucleoprotein Sm D1
AJ: Small nuclear ribonucleoprotein Sm D2
AK: Small nuclear ribonucleoprotein E
AL: Small nuclear ribonucleoprotein F
AM: LD23602p
AN: CG10419
AO: Icln
AP: Small nuclear ribonucleoprotein G
AA: Small nuclear ribonucleoprotein Sm D1
AB: Small nuclear ribonucleoprotein Sm D2
AC: Small nuclear ribonucleoprotein E
AD: Small nuclear ribonucleoprotein F
AE: LD23602p
AF: CG10419
AG: Icln
AH: Small nuclear ribonucleoprotein G
AQ: Small nuclear ribonucleoprotein Sm D1
AR: Small nuclear ribonucleoprotein Sm D2
AS: Small nuclear ribonucleoprotein E
AT: Small nuclear ribonucleoprotein F
AU: LD23602p
AV: CG10419
AW: Icln
AX: Small nuclear ribonucleoprotein G
AY: Small nuclear ribonucleoprotein Sm D1
AZ: Small nuclear ribonucleoprotein Sm D2
Aa: Small nuclear ribonucleoprotein E
Ab: Small nuclear ribonucleoprotein F
Ac: LD23602p
Ad: CG10419
Ae: Icln
Af: Small nuclear ribonucleoprotein G
Ag: Small nuclear ribonucleoprotein Sm D1
Ah: Small nuclear ribonucleoprotein Sm D2
Ai: Small nuclear ribonucleoprotein E
Aj: Small nuclear ribonucleoprotein F
Ak: LD23602p
Al: CG10419
Am: Icln
An: Small nuclear ribonucleoprotein G
Ao: Small nuclear ribonucleoprotein Sm D1
Ap: Small nuclear ribonucleoprotein Sm D2
Aq: Small nuclear ribonucleoprotein E
Ar: Small nuclear ribonucleoprotein F
As: LD23602p
At: CG10419
Au: Icln
Av: Small nuclear ribonucleoprotein G
A1: LD23602p
A2: CG10419
A3: Icln
A4: Small nuclear ribonucleoprotein G
Aw: Small nuclear ribonucleoprotein Sm D1
Ax: Small nuclear ribonucleoprotein Sm D2
Ay: Small nuclear ribonucleoprotein E
Az: Small nuclear ribonucleoprotein F
BA: Small nuclear ribonucleoprotein Sm D1
BB: Small nuclear ribonucleoprotein Sm D2
BC: Small nuclear ribonucleoprotein E
BD: Small nuclear ribonucleoprotein F
BE: LD23602p
BF: CG10419
BG: Icln
BH: Small nuclear ribonucleoprotein G
BI: Small nuclear ribonucleoprotein Sm D1
BJ: Small nuclear ribonucleoprotein Sm D2
BK: Small nuclear ribonucleoprotein E
BL: Small nuclear ribonucleoprotein F
BM: LD23602p
BN: CG10419
BO: Icln
BP: Small nuclear ribonucleoprotein G
BQ: Small nuclear ribonucleoprotein Sm D1
BR: Small nuclear ribonucleoprotein Sm D2
BS: Small nuclear ribonucleoprotein E
BT: Small nuclear ribonucleoprotein F
BU: LD23602p
BV: CG10419
BW: Icln
BX: Small nuclear ribonucleoprotein G
BY: Small nuclear ribonucleoprotein Sm D1
BZ: Small nuclear ribonucleoprotein Sm D2
Ba: Small nuclear ribonucleoprotein E
Bb: Small nuclear ribonucleoprotein F
Bc: LD23602p
Bd: CG10419
Be: Icln
Bf: Small nuclear ribonucleoprotein G
Bg: Small nuclear ribonucleoprotein Sm D1
Bh: Small nuclear ribonucleoprotein Sm D2
Bi: Small nuclear ribonucleoprotein E
Bj: Small nuclear ribonucleoprotein F
Bk: LD23602p
Bl: CG10419
Bm: Icln
Bn: Small nuclear ribonucleoprotein G
Bo: Small nuclear ribonucleoprotein Sm D1
Bp: Small nuclear ribonucleoprotein Sm D2
Bq: Small nuclear ribonucleoprotein E
Br: Small nuclear ribonucleoprotein F
Bs: LD23602p
Bt: CG10419
Bu: Icln
Bv: Small nuclear ribonucleoprotein G
B1: LD23602p
B2: CG10419
B3: Icln
B4: Small nuclear ribonucleoprotein G
Bw: Small nuclear ribonucleoprotein Sm D1
Bx: Small nuclear ribonucleoprotein Sm D2
By: Small nuclear ribonucleoprotein E
Bz: Small nuclear ribonucleoprotein F
CA: Small nuclear ribonucleoprotein Sm D1
CB: Small nuclear ribonucleoprotein Sm D2
CC: Small nuclear ribonucleoprotein E
CD: Small nuclear ribonucleoprotein F
CE: LD23602p
CF: CG10419
CG: Icln
CH: Small nuclear ribonucleoprotein G
CI: Small nuclear ribonucleoprotein Sm D1
CJ: Small nuclear ribonucleoprotein Sm D2
CK: Small nuclear ribonucleoprotein E
CL: Small nuclear ribonucleoprotein F
CM: LD23602p
CN: CG10419
CO: Icln
CP: Small nuclear ribonucleoprotein G
CQ: Small nuclear ribonucleoprotein Sm D1
CR: Small nuclear ribonucleoprotein Sm D2
CS: Small nuclear ribonucleoprotein E
CT: Small nuclear ribonucleoprotein F
CU: LD23602p
CV: CG10419
CW: Icln
CX: Small nuclear ribonucleoprotein G
CY: Small nuclear ribonucleoprotein Sm D1
CZ: Small nuclear ribonucleoprotein Sm D2
Ca: Small nuclear ribonucleoprotein E
Cb: Small nuclear ribonucleoprotein F
Cc: LD23602p
Cd: CG10419
Ce: Icln
Cf: Small nuclear ribonucleoprotein G
Cg: Small nuclear ribonucleoprotein Sm D1
Ch: Small nuclear ribonucleoprotein Sm D2
Ci: Small nuclear ribonucleoprotein E
Cj: Small nuclear ribonucleoprotein F
Ck: LD23602p
Cl: CG10419
Cm: Icln
Cn: Small nuclear ribonucleoprotein G
Co: Small nuclear ribonucleoprotein Sm D1
Cp: Small nuclear ribonucleoprotein Sm D2
Cq: Small nuclear ribonucleoprotein E
Cr: Small nuclear ribonucleoprotein F
Cs: LD23602p
Ct: CG10419
Cu: Icln
Cv: Small nuclear ribonucleoprotein G
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)2,376,864170
ポリマ－2,375,904160
非ポリマー96110
水00
1
AI: Small nuclear ribonucleoprotein Sm D1
AJ: Small nuclear ribonucleoprotein Sm D2
AK: Small nuclear ribonucleoprotein E
AL: Small nuclear ribonucleoprotein F
AM: LD23602p
AN: CG10419
AO: Icln
AP: Small nuclear ribonucleoprotein G


分子量 (理論値)分子数
合計 (水以外)118,7958
ポリマ－118,7958
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area17400 Å2
ΔGint-81 kcal/mol
Surface area33600 Å2
手法PISA
2
AA: Small nuclear ribonucleoprotein Sm D1
AB: Small nuclear ribonucleoprotein Sm D2
AC: Small nuclear ribonucleoprotein E
AD: Small nuclear ribonucleoprotein F
AE: LD23602p
AF: CG10419
AG: Icln
AH: Small nuclear ribonucleoprotein G


分子量 (理論値)分子数
合計 (水以外)118,7958
ポリマ－118,7958
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area17400 Å2
ΔGint-80 kcal/mol
Surface area33750 Å2
手法PISA
3
AQ: Small nuclear ribonucleoprotein Sm D1
AR: Small nuclear ribonucleoprotein Sm D2
AS: Small nuclear ribonucleoprotein E
AT: Small nuclear ribonucleoprotein F
AU: LD23602p
AV: CG10419
AW: Icln
AX: Small nuclear ribonucleoprotein G


分子量 (理論値)分子数
合計 (水以外)118,7958
ポリマ－118,7958
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area17370 Å2
ΔGint-79 kcal/mol
Surface area33690 Å2
手法PISA
4
AY: Small nuclear ribonucleoprotein Sm D1
AZ: Small nuclear ribonucleoprotein Sm D2
Aa: Small nuclear ribonucleoprotein E
Ab: Small nuclear ribonucleoprotein F
Ac: LD23602p
Ad: CG10419
Ae: Icln
Af: Small nuclear ribonucleoprotein G
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)118,8919
ポリマ－118,7958
非ポリマー961
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area17250 Å2
ΔGint-79 kcal/mol
Surface area33870 Å2
手法PISA
5
Ag: Small nuclear ribonucleoprotein Sm D1
Ah: Small nuclear ribonucleoprotein Sm D2
Ai: Small nuclear ribonucleoprotein E
Aj: Small nuclear ribonucleoprotein F
Ak: LD23602p
Al: CG10419
Am: Icln
An: Small nuclear ribonucleoprotein G


分子量 (理論値)分子数
合計 (水以外)118,7958
ポリマ－118,7958
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area17330 Å2
ΔGint-79 kcal/mol
Surface area33750 Å2
手法PISA
6
Ao: Small nuclear ribonucleoprotein Sm D1
Ap: Small nuclear ribonucleoprotein Sm D2
Aq: Small nuclear ribonucleoprotein E
Ar: Small nuclear ribonucleoprotein F
As: LD23602p
At: CG10419
Au: Icln
Av: Small nuclear ribonucleoprotein G
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)118,8919
ポリマ－118,7958
非ポリマー961
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area17530 Å2
ΔGint-91 kcal/mol
Surface area33710 Å2
手法PISA
7
A1: LD23602p
A2: CG10419
A3: Icln
A4: Small nuclear ribonucleoprotein G
Aw: Small nuclear ribonucleoprotein Sm D1
Ax: Small nuclear ribonucleoprotein Sm D2
Ay: Small nuclear ribonucleoprotein E
Az: Small nuclear ribonucleoprotein F
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)118,8919
ポリマ－118,7958
非ポリマー961
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area17520 Å2
ΔGint-92 kcal/mol
Surface area33870 Å2
手法PISA
8
BA: Small nuclear ribonucleoprotein Sm D1
BB: Small nuclear ribonucleoprotein Sm D2
BC: Small nuclear ribonucleoprotein E
BD: Small nuclear ribonucleoprotein F
BE: LD23602p
BF: CG10419
BG: Icln
BH: Small nuclear ribonucleoprotein G
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)118,8919
ポリマ－118,7958
非ポリマー961
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area17490 Å2
ΔGint-80 kcal/mol
Surface area33710 Å2
手法PISA
9
BI: Small nuclear ribonucleoprotein Sm D1
BJ: Small nuclear ribonucleoprotein Sm D2
BK: Small nuclear ribonucleoprotein E
BL: Small nuclear ribonucleoprotein F
BM: LD23602p
BN: CG10419
BO: Icln
BP: Small nuclear ribonucleoprotein G


分子量 (理論値)分子数
合計 (水以外)118,7958
ポリマ－118,7958
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area17340 Å2
ΔGint-79 kcal/mol
Surface area33830 Å2
手法PISA
10
BQ: Small nuclear ribonucleoprotein Sm D1
BR: Small nuclear ribonucleoprotein Sm D2
BS: Small nuclear ribonucleoprotein E
BT: Small nuclear ribonucleoprotein F
BU: LD23602p
BV: CG10419
BW: Icln
BX: Small nuclear ribonucleoprotein G
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)118,8919
ポリマ－118,7958
非ポリマー961
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area17420 Å2
ΔGint-81 kcal/mol
Surface area33680 Å2
手法PISA
11
BY: Small nuclear ribonucleoprotein Sm D1
BZ: Small nuclear ribonucleoprotein Sm D2
Ba: Small nuclear ribonucleoprotein E
Bb: Small nuclear ribonucleoprotein F
Bc: LD23602p
Bd: CG10419
Be: Icln
Bf: Small nuclear ribonucleoprotein G
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)118,8919
ポリマ－118,7958
非ポリマー961
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area17260 Å2
ΔGint-75 kcal/mol
Surface area33820 Å2
手法PISA
12
Bg: Small nuclear ribonucleoprotein Sm D1
Bh: Small nuclear ribonucleoprotein Sm D2
Bi: Small nuclear ribonucleoprotein E
Bj: Small nuclear ribonucleoprotein F
Bk: LD23602p
Bl: CG10419
Bm: Icln
Bn: Small nuclear ribonucleoprotein G


分子量 (理論値)分子数
合計 (水以外)118,7958
ポリマ－118,7958
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area17240 Å2
ΔGint-79 kcal/mol
Surface area33850 Å2
手法PISA
13
Bo: Small nuclear ribonucleoprotein Sm D1
Bp: Small nuclear ribonucleoprotein Sm D2
Bq: Small nuclear ribonucleoprotein E
Br: Small nuclear ribonucleoprotein F
Bs: LD23602p
Bt: CG10419
Bu: Icln
Bv: Small nuclear ribonucleoprotein G
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)118,8919
ポリマ－118,7958
非ポリマー961
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area17180 Å2
ΔGint-82 kcal/mol
Surface area33890 Å2
手法PISA
14
B1: LD23602p
B2: CG10419
B3: Icln
B4: Small nuclear ribonucleoprotein G
Bw: Small nuclear ribonucleoprotein Sm D1
Bx: Small nuclear ribonucleoprotein Sm D2
By: Small nuclear ribonucleoprotein E
Bz: Small nuclear ribonucleoprotein F
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)118,8919
ポリマ－118,7958
非ポリマー961
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area17110 Å2
ΔGint-78 kcal/mol
Surface area33940 Å2
手法PISA
15
CA: Small nuclear ribonucleoprotein Sm D1
CB: Small nuclear ribonucleoprotein Sm D2
CC: Small nuclear ribonucleoprotein E
CD: Small nuclear ribonucleoprotein F
CE: LD23602p
CF: CG10419
CG: Icln
CH: Small nuclear ribonucleoprotein G
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)118,8919
ポリマ－118,7958
非ポリマー961
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area17430 Å2
ΔGint-80 kcal/mol
Surface area33740 Å2
手法PISA
16
CI: Small nuclear ribonucleoprotein Sm D1
CJ: Small nuclear ribonucleoprotein Sm D2
CK: Small nuclear ribonucleoprotein E
CL: Small nuclear ribonucleoprotein F
CM: LD23602p
CN: CG10419
CO: Icln
CP: Small nuclear ribonucleoprotein G


分子量 (理論値)分子数
合計 (水以外)118,7958
ポリマ－118,7958
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area17360 Å2
ΔGint-79 kcal/mol
Surface area33770 Å2
手法PISA
17
CQ: Small nuclear ribonucleoprotein Sm D1
CR: Small nuclear ribonucleoprotein Sm D2
CS: Small nuclear ribonucleoprotein E
CT: Small nuclear ribonucleoprotein F
CU: LD23602p
CV: CG10419
CW: Icln
CX: Small nuclear ribonucleoprotein G


分子量 (理論値)分子数
合計 (水以外)118,7958
ポリマ－118,7958
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area17420 Å2
ΔGint-81 kcal/mol
Surface area33640 Å2
手法PISA
18
CY: Small nuclear ribonucleoprotein Sm D1
CZ: Small nuclear ribonucleoprotein Sm D2
Ca: Small nuclear ribonucleoprotein E
Cb: Small nuclear ribonucleoprotein F
Cc: LD23602p
Cd: CG10419
Ce: Icln
Cf: Small nuclear ribonucleoprotein G


分子量 (理論値)分子数
合計 (水以外)118,7958
ポリマ－118,7958
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area17320 Å2
ΔGint-79 kcal/mol
Surface area33730 Å2
手法PISA
19
Cg: Small nuclear ribonucleoprotein Sm D1
Ch: Small nuclear ribonucleoprotein Sm D2
Ci: Small nuclear ribonucleoprotein E
Cj: Small nuclear ribonucleoprotein F
Ck: LD23602p
Cl: CG10419
Cm: Icln
Cn: Small nuclear ribonucleoprotein G
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)118,8919
ポリマ－118,7958
非ポリマー961
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area17500 Å2
ΔGint-82 kcal/mol
Surface area33570 Å2
手法PISA
20
Co: Small nuclear ribonucleoprotein Sm D1
Cp: Small nuclear ribonucleoprotein Sm D2
Cq: Small nuclear ribonucleoprotein E
Cr: Small nuclear ribonucleoprotein F
Cs: LD23602p
Ct: CG10419
Cu: Icln
Cv: Small nuclear ribonucleoprotein G


分子量 (理論値)分子数
合計 (水以外)118,7958
ポリマ－118,7958
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area17180 Å2
ΔGint-81 kcal/mol
Surface area34040 Å2
手法PISA
単位格子
Length a, b, c (Å)150.930, 356.810, 230.750
Angle α, β, γ (deg.)90.00, 97.31, 90.00
Int Tables number4
Space group name H-MP1211

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要素

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Small nuclear ribonucleoprotein ... , 5種, 100分子 AIAAAQAYAgAoAwBABIBQBYBgBoBwCACICQCYCgCoAJABARAZAhApAxBBBJBR...

#1: タンパク質
Small nuclear ribonucleoprotein Sm D1 / Sm-D1 / Sm-D autoantigen / snRNP core protein D1


分子量: 13310.653 Da / 分子数: 20 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: SNRPD1 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: P62314
#2: タンパク質
Small nuclear ribonucleoprotein Sm D2 / Sm-D2 / snRNP core protein D2


分子量: 13551.928 Da / 分子数: 20 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: SNRPD2 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: P62316
#3: タンパク質
Small nuclear ribonucleoprotein E / snRNP-E / Sm protein E / Sm-E / SmE


分子量: 10817.601 Da / 分子数: 20 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: SNRPE / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: P62304
#4: タンパク質
Small nuclear ribonucleoprotein F / snRNP-F / Sm protein F / Sm-F / SmF


分子量: 9734.171 Da / 分子数: 20 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: SNRPF, PBSCF / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: P62306
#8: タンパク質
Small nuclear ribonucleoprotein G / snRNP-G / Sm protein G / Sm-G / SmG


分子量: 8508.084 Da / 分子数: 20 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: SNRPG, PBSCG / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: P62308

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タンパク質 , 3種, 60分子 AMAEAUAcAkAsA1BEBMBUBcBkBsB1CECMCUCcCkCsANAFAVAdAlAtA2BFBNBV...

#5: タンパク質
LD23602p / Survival motor neuron / Survival motor neuron protein SMN


分子量: 13362.475 Da / 分子数: 20 / Fragment: UNP residues 1-122 / 由来タイプ: 組換発現
由来: (組換発現) Drosophila melanogaster (キイロショウジョウバエ)
遺伝子: Smn, CG16725, Dmel_CG16725 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: Q9VV74
#6: タンパク質
CG10419


分子量: 28910.855 Da / 分子数: 20 / 由来タイプ: 組換発現
由来: (組換発現) Drosophila melanogaster (キイロショウジョウバエ)
遺伝子: Gem2, CG10419, Dmel_CG10419 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: Q9VVX0
#7: タンパク質
Icln


分子量: 20599.416 Da / 分子数: 20 / 由来タイプ: 組換発現
由来: (組換発現) Drosophila melanogaster (キイロショウジョウバエ)
遺伝子: Dmel_CG4924, icln, icln-RA / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: Q9U3W1, UniProt: A1ZAW5*PLUS

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非ポリマー , 1種, 10分子

#9: 化合物
ChemComp-SO4 / SULFATE ION / 硫酸ジアニオン


分子量: 96.063 Da / 分子数: 10 / 由来タイプ: 合成 / 式: SO4

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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: 2.59 Å3/Da / 溶媒含有率: 52.58 %
結晶化温度: 289 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 7.5
詳細: 24% PEG 4000, 10% Ethanol, 150mM NaCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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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: ESRF / ビームライン: ID14-4 / 波長: 0.9762 Å
検出器タイプ: ADSC QUANTUM 315r / 検出器: CCD / 日付: 2011年7月5日
放射モノクロメーター: XXX / 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: 0.9762 Å / 相対比: 1
反射解像度: 3.1→59.5 Å / Num. obs: 281563 / % possible obs: 98.9 % / 冗長度: 3.9 % / Biso Wilson estimate: 70.79 Å2 / Rsym value: 0.044 / Net I/σ(I): 14.3
反射 シェル
解像度 (Å)冗長度 (%)Mean I/σ(I) obsRsym valueDiffraction-ID% possible all
3.1-3.293.91.350.92815.8
4-4.23.92.310.505196.7

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解析

ソフトウェア
名称バージョン分類
MxCuBEデータ収集
PHASER位相決定
BUSTER2.10.0精密化
XDSデータ削減
XDSデータスケーリング
精密化構造決定の手法: 分子置換
開始モデル: PDB ENTRY 3S6N

3s6n
PDB 未公開エントリ


解像度: 3.1→59.47 Å / Cor.coef. Fo:Fc: 0.9214 / Cor.coef. Fo:Fc free: 0.9069 / 交差検証法: THROUGHOUT / σ(F): 0
詳細: THE XTRIAGE PROGRAM STRONGLY INDICATES A TRANSLATIONAL PSEUDO SYMMETRY
Rfactor反射数%反射Selection details
Rfree0.256 14120 5.01 %RANDOM
Rwork0.2324 ---
obs0.2336 281563 64.58 %-
原子変位パラメータBiso mean: 110.38 Å2
Baniso -1Baniso -2Baniso -3
1-8.268 Å20 Å23.6906 Å2
2---14.4779 Å20 Å2
3---6.21 Å2
Refine analyzeLuzzati coordinate error obs: 1.306 Å
精密化ステップサイクル: LAST / 解像度: 3.1→59.47 Å
タンパク質核酸リガンド溶媒全体
原子数42679 0 10 0 42689
拘束条件
Refine-IDタイプDev ideal数Restraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.01124240HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.29168080HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d44460SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes3480HARMONIC2
X-RAY DIFFRACTIONt_gen_planes17220HARMONIC5
X-RAY DIFFRACTIONt_it124240HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.85
X-RAY DIFFRACTIONt_other_torsion21.3
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion16040SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact139497SEMIHARMONIC4
LS精密化 シェル解像度: 3.1→3.18 Å / Total num. of bins used: 20
Rfactor反射数%反射
Rfree0.2061 44 5.66 %
Rwork0.2179 733 -
all0.2172 777 -
obs--64.58 %
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)
11.95920.1343-0.90873.3786-0.10651.7693-0.15040.59760.2797-0.43790.33990.62440.0631-0.3882-0.18960.1616-0.24780.192-0.15490.05380.069679.203345.6357258.7164
22.40190.80080.57422.7906-0.16341.67630.0627-0.3135-0.24060.40130.05790.01360.2734-0.3351-0.12060.06660.2157-0.0152-0.29660.1218-0.136335.5987-27.33182.3939
32.086-1.00130.62582.6436-0.47651.3693-0.12430.70770.2288-0.42830.0023-0.38580.00620.37940.1220.1103-0.3409-0.1692-0.04680.20190.234927.8282113.90430.2842
42.1571-0.64240.77652.69760.08351.74590.03860.4706-0.1392-0.38810.115-0.0983-0.0380.4581-0.1536-0.0504-0.04990.1269-0.3052-0.050.005925.102943.979831.9547
52.5971-0.64950.39751.9317-0.21970.8132-0.14811.02340.50980.1737-0.0145-0.51110.32720.21870.16260.3671-0.5103-0.47370.05460.39430.396588.01777.6524145.8506
61.9626-0.2143-0.74943.10920.34541.69850.06270.30190.3392-0.58740.1350.1734-0.1573-0.348-0.19770.2851-0.08510.1731-0.24640.1418-0.0139-39.6035115.43632.1027
71.6424-0.94130.75472.7397-0.34791.06430.09190.3142-0.1376-0.52560.1236-0.13850.12390.2068-0.21540.3375-0.19020.0987-0.2531-0.0837-0.043727.6979327.97429.9435
82.4044-0.6972-0.61113.7935-0.83353.27960.2170.46720.11830.15760.12310.3808-1.2627-0.1156-0.34010.7804-0.46490.4717-0.44830.0458-0.291420.74388.4434146.5898
91.8351-0.71621.02832.931-0.2621.32870.15250.536-0.0728-0.6115-0.0272-0.25660.19810.2885-0.12540.1604-0.3380.0593-0.3679-0.0326-0.029888.5476220.915144.4547
102.99911.43590.41033.0604-0.1491.5552-0.0728-0.69810.43130.47450.02370.56040.046-0.38830.0491-0.14370.3354-0.1611-0.2289-0.08580.072735.7267115.24182.7213
111.813-1.05130.19743.85770.97982.25480.09040.53410.14890.1835-0.0157-0.50971.1911-0.0555-0.07460.9046-0.4738-0.3064-0.42620.1104-0.337688.038478.3412144.2432
122.53250.7942-0.62753.3517-0.21861.92480.0865-0.53480.06910.67190.0027-0.4078-0.19090.4543-0.08920.0880.27660.1476-0.3672-0.11630.005-50.639944.127482.4668
132.89230.1981-0.52012.44160.43461.0251-0.1085-1.0017-0.1796-0.18610.195-0.6279-0.43390.135-0.08650.61840.42050.53390.09370.30590.137712.251680.3846197.2733
142.0020.99540.50043.8037-1.41983.52490.2039-0.4592-0.0777-0.42940.15080.32991.20780.0829-0.35460.71420.421-0.2533-0.3394-0.0417-0.4591-25.698479.6648-32.0982
152.76781.60820.03132.1778-0.1761.102-0.3607-0.84310.9186-0.19480.2420.59070.2933-0.19420.11880.51570.5089-0.4677-0.1307-0.39310.4939-25.41477.7533-30.7718
162.5467-0.2143-0.62942.5869-0.85841.4576-0.15160.949-0.48820.46480.22071.0351-0.769-0.2465-0.06910.6393-0.42310.5219-0.1364-0.28490.25120.725880.4463144.8141
172.7483-0.764-0.25572.9670.15171.4688-0.08330.6701-0.3699-0.43520.16520.63170.0172-0.3607-0.08180.0809-0.20740.3061-0.0901-0.06080.388282.1646-27.1476260.4433
181.94550.3777-0.94743.00270.15671.5462-0.13030.47780.3622-0.38650.32870.4422-0.0429-0.3779-0.19840.1264-0.39290.1548-0.23920.15450.141118.5571295.388144.1518
192.1334-0.0105-0.19523.9178-0.61911.719-0.25360.57790.33950.37350.32910.7149-0.4451-0.0892-0.07540.7127-0.47110.4899-0.18460.0885-0.17879.6767188.206258.4364
202.7396-0.4102-1.00812.47760.3331.4451-0.13710.9862-0.335-0.22960.01190.61630.0057-0.49280.12510.1034-0.42430.40910.0575-0.27620.405618.3892152.557144.7886
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ Bw|* Bx|* By|* Bz|* B1|* B2|* B3|* B4|* }Bw1000 - 1081
2X-RAY DIFFRACTION1{ Bw|* Bx|* By|* Bz|* B1|* B2|* B3|* B4|* }Bx2000 - 2099
3X-RAY DIFFRACTION1{ Bw|* Bx|* By|* Bz|* B1|* B2|* B3|* B4|* }By3000 - 3076
4X-RAY DIFFRACTION1{ Bw|* Bx|* By|* Bz|* B1|* B2|* B3|* B4|* }Bz4000 - 4070
5X-RAY DIFFRACTION1{ Bw|* Bx|* By|* Bz|* B1|* B2|* B3|* B4|* }B17000 - 7016
6X-RAY DIFFRACTION1{ Bw|* Bx|* By|* Bz|* B1|* B2|* B3|* B4|* }B28000 - 8215
7X-RAY DIFFRACTION1{ Bw|* Bx|* By|* Bz|* B1|* B2|* B3|* B4|* }B36000 - 6167
8X-RAY DIFFRACTION1{ Bw|* Bx|* By|* Bz|* B1|* B2|* B3|* B4|* }B45000 - 5069
9X-RAY DIFFRACTION2{ AI|* AJ|* AK|* AL|* AM|* AN|* AO|* AP|* }AI1000 - 1081
10X-RAY DIFFRACTION2{ AI|* AJ|* AK|* AL|* AM|* AN|* AO|* AP|* }AJ2000 - 2099
11X-RAY DIFFRACTION2{ AI|* AJ|* AK|* AL|* AM|* AN|* AO|* AP|* }AK3000 - 3076
12X-RAY DIFFRACTION2{ AI|* AJ|* AK|* AL|* AM|* AN|* AO|* AP|* }AL4000 - 4070
13X-RAY DIFFRACTION2{ AI|* AJ|* AK|* AL|* AM|* AN|* AO|* AP|* }AM7000 - 7016
14X-RAY DIFFRACTION2{ AI|* AJ|* AK|* AL|* AM|* AN|* AO|* AP|* }AN8000 - 8215
15X-RAY DIFFRACTION2{ AI|* AJ|* AK|* AL|* AM|* AN|* AO|* AP|* }AO6000 - 6167
16X-RAY DIFFRACTION2{ AI|* AJ|* AK|* AL|* AM|* AN|* AO|* AP|* }AP5000 - 5069
17X-RAY DIFFRACTION3{ CA|* CB|* CC|* CD|* CE|* CF|* CG|* CH|* }CA1000 - 1081
18X-RAY DIFFRACTION3{ CA|* CB|* CC|* CD|* CE|* CF|* CG|* CH|* }CB2000 - 2099
19X-RAY DIFFRACTION3{ CA|* CB|* CC|* CD|* CE|* CF|* CG|* CH|* }CC3000 - 3076
20X-RAY DIFFRACTION3{ CA|* CB|* CC|* CD|* CE|* CF|* CG|* CH|* }CD4000 - 4070
21X-RAY DIFFRACTION3{ CA|* CB|* CC|* CD|* CE|* CF|* CG|* CH|* }CE7000 - 7016
22X-RAY DIFFRACTION3{ CA|* CB|* CC|* CD|* CE|* CF|* CG|* CH|* }CF8000 - 8215
23X-RAY DIFFRACTION3{ CA|* CB|* CC|* CD|* CE|* CF|* CG|* CH|* }CG6000 - 6167
24X-RAY DIFFRACTION3{ CA|* CB|* CC|* CD|* CE|* CF|* CG|* CH|* }CH5000 - 5069
25X-RAY DIFFRACTION4{ AA|* AB|* AC|* AD|* AE|* AF|* AG|* AH|* }AA1000 - 1081
26X-RAY DIFFRACTION4{ AA|* AB|* AC|* AD|* AE|* AF|* AG|* AH|* }AB2000 - 2099
27X-RAY DIFFRACTION4{ AA|* AB|* AC|* AD|* AE|* AF|* AG|* AH|* }AC3000 - 3076
28X-RAY DIFFRACTION4{ AA|* AB|* AC|* AD|* AE|* AF|* AG|* AH|* }AD4000 - 4070
29X-RAY DIFFRACTION4{ AA|* AB|* AC|* AD|* AE|* AF|* AG|* AH|* }AE7000 - 7016
30X-RAY DIFFRACTION4{ AA|* AB|* AC|* AD|* AE|* AF|* AG|* AH|* }AF8000 - 8215
31X-RAY DIFFRACTION4{ AA|* AB|* AC|* AD|* AE|* AF|* AG|* AH|* }AG6000 - 6167
32X-RAY DIFFRACTION4{ AA|* AB|* AC|* AD|* AE|* AF|* AG|* AH|* }AH5000 - 5069
33X-RAY DIFFRACTION5{ CI|* CJ|* CK|* CL|* CM|* CN|* CO|* CP|* }CI1000 - 1081
34X-RAY DIFFRACTION5{ CI|* CJ|* CK|* CL|* CM|* CN|* CO|* CP|* }CJ2000 - 2099
35X-RAY DIFFRACTION5{ CI|* CJ|* CK|* CL|* CM|* CN|* CO|* CP|* }CK3000 - 3076
36X-RAY DIFFRACTION5{ CI|* CJ|* CK|* CL|* CM|* CN|* CO|* CP|* }CL4000 - 4070
37X-RAY DIFFRACTION5{ CI|* CJ|* CK|* CL|* CM|* CN|* CO|* CP|* }CM7000 - 7016
38X-RAY DIFFRACTION5{ CI|* CJ|* CK|* CL|* CM|* CN|* CO|* CP|* }CN8000 - 8215
39X-RAY DIFFRACTION5{ CI|* CJ|* CK|* CL|* CM|* CN|* CO|* CP|* }CO6000 - 6167
40X-RAY DIFFRACTION5{ CI|* CJ|* CK|* CL|* CM|* CN|* CO|* CP|* }CP5000 - 5069
41X-RAY DIFFRACTION6{ AQ|* AR|* AS|* AT|* AU|* AV|* AW|* AX|* }AQ1000 - 1081
42X-RAY DIFFRACTION6{ AQ|* AR|* AS|* AT|* AU|* AV|* AW|* AX|* }AR2000 - 2099
43X-RAY DIFFRACTION6{ AQ|* AR|* AS|* AT|* AU|* AV|* AW|* AX|* }AS3000 - 3076
44X-RAY DIFFRACTION6{ AQ|* AR|* AS|* AT|* AU|* AV|* AW|* AX|* }AT4000 - 4070
45X-RAY DIFFRACTION6{ AQ|* AR|* AS|* AT|* AU|* AV|* AW|* AX|* }AU7000 - 7016
46X-RAY DIFFRACTION6{ AQ|* AR|* AS|* AT|* AU|* AV|* AW|* AX|* }AV8000 - 8215
47X-RAY DIFFRACTION6{ AQ|* AR|* AS|* AT|* AU|* AV|* AW|* AX|* }AW6000 - 6126
48X-RAY DIFFRACTION6{ AQ|* AR|* AS|* AT|* AU|* AV|* AW|* AX|* }AX5000 - 5069
49X-RAY DIFFRACTION7{ CQ|* CR|* CS|* CT|* CU|* CV|* CW|* CX|* }CQ1000 - 1081
50X-RAY DIFFRACTION7{ CQ|* CR|* CS|* CT|* CU|* CV|* CW|* CX|* }CR2000 - 2099
51X-RAY DIFFRACTION7{ CQ|* CR|* CS|* CT|* CU|* CV|* CW|* CX|* }CS3000 - 3076
52X-RAY DIFFRACTION7{ CQ|* CR|* CS|* CT|* CU|* CV|* CW|* CX|* }CT4000 - 4070
53X-RAY DIFFRACTION7{ CQ|* CR|* CS|* CT|* CU|* CV|* CW|* CX|* }CU7000 - 7016
54X-RAY DIFFRACTION7{ CQ|* CR|* CS|* CT|* CU|* CV|* CW|* CX|* }CV8000 - 8215
55X-RAY DIFFRACTION7{ CQ|* CR|* CS|* CT|* CU|* CV|* CW|* CX|* }CW6000 - 6126
56X-RAY DIFFRACTION7{ CQ|* CR|* CS|* CT|* CU|* CV|* CW|* CX|* }CX5000 - 5069
57X-RAY DIFFRACTION8{ AY|* AZ|* Aa|* Ab|* Ac|* Ad|* Ae|* Af|* }AY1000 - 1081
58X-RAY DIFFRACTION8{ AY|* AZ|* Aa|* Ab|* Ac|* Ad|* Ae|* Af|* }AZ2000 - 2099
59X-RAY DIFFRACTION8{ AY|* AZ|* Aa|* Ab|* Ac|* Ad|* Ae|* Af|* }Aa3000 - 3076
60X-RAY DIFFRACTION8{ AY|* AZ|* Aa|* Ab|* Ac|* Ad|* Ae|* Af|* }Ab4000 - 4070
61X-RAY DIFFRACTION8{ AY|* AZ|* Aa|* Ab|* Ac|* Ad|* Ae|* Af|* }Ac7000 - 7016
62X-RAY DIFFRACTION8{ AY|* AZ|* Aa|* Ab|* Ac|* Ad|* Ae|* Af|* }Ad8000 - 8215
63X-RAY DIFFRACTION8{ AY|* AZ|* Aa|* Ab|* Ac|* Ad|* Ae|* Af|* }Ae6000 - 6126
64X-RAY DIFFRACTION8{ AY|* AZ|* Aa|* Ab|* Ac|* Ad|* Ae|* Af|* }Af5000 - 5069
65X-RAY DIFFRACTION9{ CY|* CZ|* Ca|* Cb|* Cc|* Cd|* Ce|* Cf|* }CY1000 - 1081
66X-RAY DIFFRACTION9{ CY|* CZ|* Ca|* Cb|* Cc|* Cd|* Ce|* Cf|* }CZ2000 - 2099
67X-RAY DIFFRACTION9{ CY|* CZ|* Ca|* Cb|* Cc|* Cd|* Ce|* Cf|* }Ca3000 - 3076
68X-RAY DIFFRACTION9{ CY|* CZ|* Ca|* Cb|* Cc|* Cd|* Ce|* Cf|* }Cb4000 - 4070
69X-RAY DIFFRACTION9{ CY|* CZ|* Ca|* Cb|* Cc|* Cd|* Ce|* Cf|* }Cc7000 - 7016
70X-RAY DIFFRACTION9{ CY|* CZ|* Ca|* Cb|* Cc|* Cd|* Ce|* Cf|* }Cd8000 - 8215
71X-RAY DIFFRACTION9{ CY|* CZ|* Ca|* Cb|* Cc|* Cd|* Ce|* Cf|* }Ce6000 - 6126
72X-RAY DIFFRACTION9{ CY|* CZ|* Ca|* Cb|* Cc|* Cd|* Ce|* Cf|* }Cf5000 - 5069
73X-RAY DIFFRACTION10{ Ag|* Ah|* Ai|* Aj|* Ak|* Al|* Am|* An|* }Ag1000 - 1081
74X-RAY DIFFRACTION10{ Ag|* Ah|* Ai|* Aj|* Ak|* Al|* Am|* An|* }Ah2000 - 2099
75X-RAY DIFFRACTION10{ Ag|* Ah|* Ai|* Aj|* Ak|* Al|* Am|* An|* }Ai3000 - 3076
76X-RAY DIFFRACTION10{ Ag|* Ah|* Ai|* Aj|* Ak|* Al|* Am|* An|* }Aj4000 - 4070
77X-RAY DIFFRACTION10{ Ag|* Ah|* Ai|* Aj|* Ak|* Al|* Am|* An|* }Ak7000 - 7016
78X-RAY DIFFRACTION10{ Ag|* Ah|* Ai|* Aj|* Ak|* Al|* Am|* An|* }Al8000 - 8215
79X-RAY DIFFRACTION10{ Ag|* Ah|* Ai|* Aj|* Ak|* Al|* Am|* An|* }Am6000 - 6126
80X-RAY DIFFRACTION10{ Ag|* Ah|* Ai|* Aj|* Ak|* Al|* Am|* An|* }An5000 - 5069
81X-RAY DIFFRACTION11{ Cg|* Ch|* Ci|* Cj|* Ck|* Cl|* Cm|* Cn|* }Cg1000 - 1081
82X-RAY DIFFRACTION11{ Cg|* Ch|* Ci|* Cj|* Ck|* Cl|* Cm|* Cn|* }Ch2000 - 2099
83X-RAY DIFFRACTION11{ Cg|* Ch|* Ci|* Cj|* Ck|* Cl|* Cm|* Cn|* }Ci3000 - 3076
84X-RAY DIFFRACTION11{ Cg|* Ch|* Ci|* Cj|* Ck|* Cl|* Cm|* Cn|* }Cj4000 - 4070
85X-RAY DIFFRACTION11{ Cg|* Ch|* Ci|* Cj|* Ck|* Cl|* Cm|* Cn|* }Ck7000 - 7016
86X-RAY DIFFRACTION11{ Cg|* Ch|* Ci|* Cj|* Ck|* Cl|* Cm|* Cn|* }Cl8000 - 8215
87X-RAY DIFFRACTION11{ Cg|* Ch|* Ci|* Cj|* Ck|* Cl|* Cm|* Cn|* }Cm6000 - 6126
88X-RAY DIFFRACTION11{ Cg|* Ch|* Ci|* Cj|* Ck|* Cl|* Cm|* Cn|* }Cn5000 - 5069
89X-RAY DIFFRACTION12{ Ao|* Ap|* Aq|* Ar|* As|* At|* Au|* Av|* }Ao1000 - 1081
90X-RAY DIFFRACTION12{ Ao|* Ap|* Aq|* Ar|* As|* At|* Au|* Av|* }Ap2000 - 2099
91X-RAY DIFFRACTION12{ Ao|* Ap|* Aq|* Ar|* As|* At|* Au|* Av|* }Aq3000 - 3076
92X-RAY DIFFRACTION12{ Ao|* Ap|* Aq|* Ar|* As|* At|* Au|* Av|* }Ar4000 - 4070
93X-RAY DIFFRACTION12{ Ao|* Ap|* Aq|* Ar|* As|* At|* Au|* Av|* }As7000 - 7016
94X-RAY DIFFRACTION12{ Ao|* Ap|* Aq|* Ar|* As|* At|* Au|* Av|* }At8000 - 8215
95X-RAY DIFFRACTION12{ Ao|* Ap|* Aq|* Ar|* As|* At|* Au|* Av|* }Au6000 - 6126
96X-RAY DIFFRACTION12{ Ao|* Ap|* Aq|* Ar|* As|* At|* Au|* Av|* }Av5000 - 5069
97X-RAY DIFFRACTION13{ Co|* Cp|* Cq|* Cr|* Cs|* Ct|* Cu|* Cv|* }Co1000 - 1081
98X-RAY DIFFRACTION13{ Co|* Cp|* Cq|* Cr|* Cs|* Ct|* Cu|* Cv|* }Cp2000 - 2099
99X-RAY DIFFRACTION13{ Co|* Cp|* Cq|* Cr|* Cs|* Ct|* Cu|* Cv|* }Cq3000 - 3076
100X-RAY DIFFRACTION13{ Co|* Cp|* Cq|* Cr|* Cs|* Ct|* Cu|* Cv|* }Cr4000 - 4070
101X-RAY DIFFRACTION13{ Co|* Cp|* Cq|* Cr|* Cs|* Ct|* Cu|* Cv|* }Cs7000 - 7016
102X-RAY DIFFRACTION13{ Co|* Cp|* Cq|* Cr|* Cs|* Ct|* Cu|* Cv|* }Ct8000 - 8215
103X-RAY DIFFRACTION13{ Co|* Cp|* Cq|* Cr|* Cs|* Ct|* Cu|* Cv|* }Cu6000 - 6126
104X-RAY DIFFRACTION13{ Co|* Cp|* Cq|* Cr|* Cs|* Ct|* Cu|* Cv|* }Cv5000 - 5069
105X-RAY DIFFRACTION14{ Aw|* Ax|* Ay|* Az|* A1|* A2|* A3|* A4|* }Aw1000 - 1081
106X-RAY DIFFRACTION14{ Aw|* Ax|* Ay|* Az|* A1|* A2|* A3|* A4|* }Ax2000 - 2099
107X-RAY DIFFRACTION14{ Aw|* Ax|* Ay|* Az|* A1|* A2|* A3|* A4|* }Ay3000 - 3076
108X-RAY DIFFRACTION14{ Aw|* Ax|* Ay|* Az|* A1|* A2|* A3|* A4|* }Az4000 - 4070
109X-RAY DIFFRACTION14{ Aw|* Ax|* Ay|* Az|* A1|* A2|* A3|* A4|* }A17000 - 7016
110X-RAY DIFFRACTION14{ Aw|* Ax|* Ay|* Az|* A1|* A2|* A3|* A4|* }A28000 - 8215
111X-RAY DIFFRACTION14{ Aw|* Ax|* Ay|* Az|* A1|* A2|* A3|* A4|* }A36000 - 6126
112X-RAY DIFFRACTION14{ Aw|* Ax|* Ay|* Az|* A1|* A2|* A3|* A4|* }A45000 - 5069
113X-RAY DIFFRACTION15{ BA|* BB|* BC|* BD|* BE|* BF|* BG|* BH|* }BA1000 - 1081
114X-RAY DIFFRACTION15{ BA|* BB|* BC|* BD|* BE|* BF|* BG|* BH|* }BB2000 - 2099
115X-RAY DIFFRACTION15{ BA|* BB|* BC|* BD|* BE|* BF|* BG|* BH|* }BC3000 - 3076
116X-RAY DIFFRACTION15{ BA|* BB|* BC|* BD|* BE|* BF|* BG|* BH|* }BD4000 - 4070
117X-RAY DIFFRACTION15{ BA|* BB|* BC|* BD|* BE|* BF|* BG|* BH|* }BE7000 - 7016
118X-RAY DIFFRACTION15{ BA|* BB|* BC|* BD|* BE|* BF|* BG|* BH|* }BF8000 - 8215
119X-RAY DIFFRACTION15{ BA|* BB|* BC|* BD|* BE|* BF|* BG|* BH|* }BG5000 - 5069
120X-RAY DIFFRACTION15{ BA|* BB|* BC|* BD|* BE|* BF|* BG|* BH|* }BG6000 - 6126
121X-RAY DIFFRACTION16{ BI|* BJ|* BK|* BL|* BM|* BN|* BO|* BP|* }BI1000 - 1081
122X-RAY DIFFRACTION16{ BI|* BJ|* BK|* BL|* BM|* BN|* BO|* BP|* }BJ2000 - 2099
123X-RAY DIFFRACTION16{ BI|* BJ|* BK|* BL|* BM|* BN|* BO|* BP|* }BK3000 - 3076
124X-RAY DIFFRACTION16{ BI|* BJ|* BK|* BL|* BM|* BN|* BO|* BP|* }BL4000 - 4070
125X-RAY DIFFRACTION16{ BI|* BJ|* BK|* BL|* BM|* BN|* BO|* BP|* }BM7000 - 7016
126X-RAY DIFFRACTION16{ BI|* BJ|* BK|* BL|* BM|* BN|* BO|* BP|* }BN8000 - 8215
127X-RAY DIFFRACTION16{ BI|* BJ|* BK|* BL|* BM|* BN|* BO|* BP|* }BO6000 - 6126
128X-RAY DIFFRACTION16{ BI|* BJ|* BK|* BL|* BM|* BN|* BO|* BP|* }BP5000 - 5069
129X-RAY DIFFRACTION17{ BQ|* BR|* BS|* BT|* BU|* BV|* BW|* BX|* }BQ1000 - 1081
130X-RAY DIFFRACTION17{ BQ|* BR|* BS|* BT|* BU|* BV|* BW|* BX|* }BR2000 - 2099
131X-RAY DIFFRACTION17{ BQ|* BR|* BS|* BT|* BU|* BV|* BW|* BX|* }BS3000 - 3076
132X-RAY DIFFRACTION17{ BQ|* BR|* BS|* BT|* BU|* BV|* BW|* BX|* }BT4000 - 4070
133X-RAY DIFFRACTION17{ BQ|* BR|* BS|* BT|* BU|* BV|* BW|* BX|* }BU7000 - 7016
134X-RAY DIFFRACTION17{ BQ|* BR|* BS|* BT|* BU|* BV|* BW|* BX|* }BV8000 - 8215
135X-RAY DIFFRACTION17{ BQ|* BR|* BS|* BT|* BU|* BV|* BW|* BX|* }BW6000 - 6126
136X-RAY DIFFRACTION17{ BQ|* BR|* BS|* BT|* BU|* BV|* BW|* BX|* }BX5000 - 5069
137X-RAY DIFFRACTION18{ BY|* BZ|* Ba|* Bb|* Bc|* Bd|* Be|* Bf|* }BY1000 - 1081
138X-RAY DIFFRACTION18{ BY|* BZ|* Ba|* Bb|* Bc|* Bd|* Be|* Bf|* }BZ2000 - 2099
139X-RAY DIFFRACTION18{ BY|* BZ|* Ba|* Bb|* Bc|* Bd|* Be|* Bf|* }Ba3000 - 3076
140X-RAY DIFFRACTION18{ BY|* BZ|* Ba|* Bb|* Bc|* Bd|* Be|* Bf|* }Bb4000 - 4070
141X-RAY DIFFRACTION18{ BY|* BZ|* Ba|* Bb|* Bc|* Bd|* Be|* Bf|* }Bc7000 - 7016
142X-RAY DIFFRACTION18{ BY|* BZ|* Ba|* Bb|* Bc|* Bd|* Be|* Bf|* }Bd8000 - 8215
143X-RAY DIFFRACTION18{ BY|* BZ|* Ba|* Bb|* Bc|* Bd|* Be|* Bf|* }Be6000 - 6126
144X-RAY DIFFRACTION18{ BY|* BZ|* Ba|* Bb|* Bc|* Bd|* Be|* Bf|* }Bf5000 - 5069
145X-RAY DIFFRACTION19{ Bg|* Bh|* Bi|* Bj|* Bk|* Bl|* Bm|* Bn|* }Bg1000 - 1081
146X-RAY DIFFRACTION19{ Bg|* Bh|* Bi|* Bj|* Bk|* Bl|* Bm|* Bn|* }Bh2000 - 2099
147X-RAY DIFFRACTION19{ Bg|* Bh|* Bi|* Bj|* Bk|* Bl|* Bm|* Bn|* }Bi3000 - 3076
148X-RAY DIFFRACTION19{ Bg|* Bh|* Bi|* Bj|* Bk|* Bl|* Bm|* Bn|* }Bj4000 - 4070
149X-RAY DIFFRACTION19{ Bg|* Bh|* Bi|* Bj|* Bk|* Bl|* Bm|* Bn|* }Bk7000 - 7016
150X-RAY DIFFRACTION19{ Bg|* Bh|* Bi|* Bj|* Bk|* Bl|* Bm|* Bn|* }Bl8000 - 8215
151X-RAY DIFFRACTION19{ Bg|* Bh|* Bi|* Bj|* Bk|* Bl|* Bm|* Bn|* }Bm6000 - 6126
152X-RAY DIFFRACTION19{ Bg|* Bh|* Bi|* Bj|* Bk|* Bl|* Bm|* Bn|* }Bn5000 - 5069
153X-RAY DIFFRACTION20{ Bo|* Bp|* Bq|* Br|* Bs|* Bt|* Bu|* Bv|* }Bo1000 - 1081
154X-RAY DIFFRACTION20{ Bo|* Bp|* Bq|* Br|* Bs|* Bt|* Bu|* Bv|* }Bp2000 - 2099
155X-RAY DIFFRACTION20{ Bo|* Bp|* Bq|* Br|* Bs|* Bt|* Bu|* Bv|* }Bq3000 - 3076
156X-RAY DIFFRACTION20{ Bo|* Bp|* Bq|* Br|* Bs|* Bt|* Bu|* Bv|* }Br4000 - 4070
157X-RAY DIFFRACTION20{ Bo|* Bp|* Bq|* Br|* Bs|* Bt|* Bu|* Bv|* }Bs7000 - 7016
168X-RAY DIFFRACTION20{ Bo|* Bp|* Bq|* Br|* Bs|* Bt|* Bu|* Bv|* }Bt8000 - 8215
169X-RAY DIFFRACTION20{ Bo|* Bp|* Bq|* Br|* Bs|* Bt|* Bu|* Bv|* }Bu6000 - 6126
160X-RAY DIFFRACTION20{ Bo|* Bp|* Bq|* Br|* Bs|* Bt|* Bu|* Bv|* }Bv5000 - 5069

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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

他の情報も見る