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- PDB-4wzj: Spliceosomal U4 snRNP core domain -

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基本情報

登録情報
データベース: PDB / ID: 4wzj
タイトルSpliceosomal U4 snRNP core domain
要素
  • (Small nuclear ribonucleoprotein ...) x 6
  • Small nuclear ribonucleoprotein-associated proteins B and B'
  • U4 small nuclear RNA variant: Native sequence 85-145, of which nucleotides 97-104 are replaced with GAAA tetraloop and nucleotides 134-137 are replaced with GAAA tetraloop receptor.
キーワードSPLICING / Splicing-RNA complex / pre-mRNA splicing / snRNP biogenesis / Sm site binding
機能・相同性
機能・相同性情報


U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / U7 snRNP / histone pre-mRNA 3'end processing complex / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / protein methylation / U12-type spliceosomal complex / methylosome ...U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / U7 snRNP / histone pre-mRNA 3'end processing complex / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / protein methylation / U12-type spliceosomal complex / methylosome / 7-methylguanosine cap hypermethylation / U1 snRNP binding / pICln-Sm protein complex / snRNP binding / small nuclear ribonucleoprotein complex / SMN-Sm protein complex / telomerase RNA binding / spliceosomal tri-snRNP complex / telomerase holoenzyme complex / P granule / U2-type spliceosomal complex / U2-type precatalytic spliceosome / commitment complex / U2-type prespliceosome assembly / U2-type catalytic step 2 spliceosome / U4 snRNP / U2 snRNP / RNA Polymerase II Transcription Termination / U1 snRNP / U2-type prespliceosome / precatalytic spliceosome / mRNA Splicing - Minor Pathway / spliceosomal complex assembly / U5 snRNP / spliceosomal snRNP assembly / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / spliceosomal complex / mRNA splicing, via spliceosome / snRNP Assembly / SARS-CoV-2 modulates host translation machinery / nuclear body / enzyme binding / RNA binding / extracellular exosome / nucleoplasm / nucleus / cytosol / cytoplasm
類似検索 - 分子機能
Small ribonucleoprotein associated, SmB/SmN / Small nuclear ribonucleoprotein D1 / : / Small nuclear ribonucleoprotein Sm D3 / Small nuclear ribonucleoprotein Sm D2 / Small nuclear ribonucleoprotein E / Small nuclear ribonucleoprotein G / Small nuclear ribonucleoprotein F / Like-Sm (LSM) domain containing protein, LSm4/SmD1/SmD3 / Sm-like protein Lsm7/SmG ...Small ribonucleoprotein associated, SmB/SmN / Small nuclear ribonucleoprotein D1 / : / Small nuclear ribonucleoprotein Sm D3 / Small nuclear ribonucleoprotein Sm D2 / Small nuclear ribonucleoprotein E / Small nuclear ribonucleoprotein G / Small nuclear ribonucleoprotein F / 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
類似検索 - ドメイン・相同性
RNA / RNA (> 10) / Small nuclear ribonucleoprotein-associated proteins B and B' / Small nuclear ribonucleoprotein E / Small nuclear ribonucleoprotein F / Small nuclear ribonucleoprotein G / Small nuclear ribonucleoprotein Sm D1 / Small nuclear ribonucleoprotein Sm D2 / Small nuclear ribonucleoprotein Sm D3
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 / 分子置換 / 解像度: 3.6 Å
データ登録者Leung, A.K.W. / Nagai, K. / Li, J.
引用
ジャーナル: Nature / 年: 2011
タイトル: Structure of the spliceosomal U4 snRNP core domain and its implication for snRNP biogenesis.
著者: Leung, A.K. / Nagai, K. / Li, J.
#1: ジャーナル: Cell(Cambridge,Mass.) / 年: 1999
タイトル: Crystal structures of two Sm protein complexes and their implications for the assembly of the spliceosomal snRNPs.
著者: Kambach, C. / Walke, S. / Young, R. / Avis, J.M. / de la Fortelle, E. / Raker, V.A. / Luhrmann, R. / Li, J. / Nagai, K.
#2: ジャーナル: Embo J. / 年: 2001
タイトル: RNA binding in an Sm core domain: X-ray structure and functional analysis of an archaeal Sm protein complex.
著者: Toro, I. / Thore, S. / Mayer, C. / Basquin, J. / Seraphin, B. / Suck, D.
#3: ジャーナル: Elife / 年: 2015
タイトル: Crystal structure of human U1 snRNP, a small nuclear ribonucleoprotein particle, reveals the mechanism of 5' splice site recognition.
著者: Kondo, Y. / Oubridge, C. / van Roon, A.M. / Nagai, K.
#4: ジャーナル: Acta Crystallogr.,Sect.D / 年: 2016
タイトル: Re-refinement of the spliceosomal U4 snRNP core-domain structure
著者: Li, J. / Leung, A.K. / Kondo, Y. / Oubridge, C. / Nagai, K.
履歴
登録2014年11月19日登録サイト: RCSB / 処理サイト: PDBE
置き換え2015年1月14日ID: 4V5U
改定 1.02015年1月14日Provider: repository / タイプ: Initial release
改定 1.12015年4月8日Group: Database references / Structure summary
改定 1.22016年1月13日Group: Database references
改定 1.32018年4月18日Group: Data collection / Database references / Source and taxonomy
カテゴリ: citation / citation_author / entity_src_gen
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
改定 1.42024年1月10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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

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集合体

登録構造単位
A: Small nuclear ribonucleoprotein Sm D3
B: Small nuclear ribonucleoprotein-associated proteins B and B'
C: Small nuclear ribonucleoprotein Sm D1
D: Small nuclear ribonucleoprotein Sm D2
F: Small nuclear ribonucleoprotein F
E: Small nuclear ribonucleoprotein E
G: Small nuclear ribonucleoprotein G
H: Small nuclear ribonucleoprotein Sm D3
I: Small nuclear ribonucleoprotein-associated proteins B and B'
J: Small nuclear ribonucleoprotein Sm D1
K: Small nuclear ribonucleoprotein Sm D2
M: Small nuclear ribonucleoprotein F
L: Small nuclear ribonucleoprotein E
N: Small nuclear ribonucleoprotein G
O: Small nuclear ribonucleoprotein Sm D3
P: Small nuclear ribonucleoprotein-associated proteins B and B'
Q: Small nuclear ribonucleoprotein Sm D1
R: Small nuclear ribonucleoprotein Sm D2
T: Small nuclear ribonucleoprotein F
S: Small nuclear ribonucleoprotein E
U: Small nuclear ribonucleoprotein G
AA: Small nuclear ribonucleoprotein Sm D3
BB: Small nuclear ribonucleoprotein-associated proteins B and B'
CC: Small nuclear ribonucleoprotein Sm D1
DD: Small nuclear ribonucleoprotein Sm D2
FF: Small nuclear ribonucleoprotein F
EE: Small nuclear ribonucleoprotein E
GG: Small nuclear ribonucleoprotein G
HH: Small nuclear ribonucleoprotein Sm D3
II: Small nuclear ribonucleoprotein-associated proteins B and B'
JJ: Small nuclear ribonucleoprotein Sm D1
KK: Small nuclear ribonucleoprotein Sm D2
MM: Small nuclear ribonucleoprotein F
LL: Small nuclear ribonucleoprotein E
NN: Small nuclear ribonucleoprotein G
OO: Small nuclear ribonucleoprotein Sm D3
PP: Small nuclear ribonucleoprotein-associated proteins B and B'
QQ: Small nuclear ribonucleoprotein Sm D1
RR: Small nuclear ribonucleoprotein Sm D2
TT: Small nuclear ribonucleoprotein F
SS: Small nuclear ribonucleoprotein E
UU: Small nuclear ribonucleoprotein G
AAA: Small nuclear ribonucleoprotein Sm D3
BBB: Small nuclear ribonucleoprotein-associated proteins B and B'
CCC: Small nuclear ribonucleoprotein Sm D1
DDD: Small nuclear ribonucleoprotein Sm D2
FFF: Small nuclear ribonucleoprotein F
EEE: Small nuclear ribonucleoprotein E
GGG: Small nuclear ribonucleoprotein G
HHH: Small nuclear ribonucleoprotein Sm D3
III: Small nuclear ribonucleoprotein-associated proteins B and B'
JJJ: Small nuclear ribonucleoprotein Sm D1
KKK: Small nuclear ribonucleoprotein Sm D2
MMM: Small nuclear ribonucleoprotein F
LLL: Small nuclear ribonucleoprotein E
NNN: Small nuclear ribonucleoprotein G
OOO: Small nuclear ribonucleoprotein Sm D3
PPP: Small nuclear ribonucleoprotein-associated proteins B and B'
QQQ: Small nuclear ribonucleoprotein Sm D1
RRR: Small nuclear ribonucleoprotein Sm D2
TTT: Small nuclear ribonucleoprotein F
SSS: Small nuclear ribonucleoprotein E
UUU: Small nuclear ribonucleoprotein G
AAAA: Small nuclear ribonucleoprotein Sm D3
BBBB: Small nuclear ribonucleoprotein-associated proteins B and B'
CCCC: Small nuclear ribonucleoprotein Sm D1
DDDD: Small nuclear ribonucleoprotein Sm D2
FFFF: Small nuclear ribonucleoprotein F
EEEE: Small nuclear ribonucleoprotein E
GGGG: Small nuclear ribonucleoprotein G
HHHH: Small nuclear ribonucleoprotein Sm D3
IIII: Small nuclear ribonucleoprotein-associated proteins B and B'
JJJJ: Small nuclear ribonucleoprotein Sm D1
KKKK: Small nuclear ribonucleoprotein Sm D2
MMMM: Small nuclear ribonucleoprotein F
LLLL: Small nuclear ribonucleoprotein E
NNNN: Small nuclear ribonucleoprotein G
OOOO: Small nuclear ribonucleoprotein Sm D3
PPPP: Small nuclear ribonucleoprotein-associated proteins B and B'
QQQQ: Small nuclear ribonucleoprotein Sm D1
RRRR: Small nuclear ribonucleoprotein Sm D2
TTTT: Small nuclear ribonucleoprotein F
SSSS: Small nuclear ribonucleoprotein E
UUUU: Small nuclear ribonucleoprotein G
V: U4 small nuclear RNA variant: Native sequence 85-145, of which nucleotides 97-104 are replaced with GAAA tetraloop and nucleotides 134-137 are replaced with GAAA tetraloop receptor.
X: U4 small nuclear RNA variant: Native sequence 85-145, of which nucleotides 97-104 are replaced with GAAA tetraloop and nucleotides 134-137 are replaced with GAAA tetraloop receptor.
Y: U4 small nuclear RNA variant: Native sequence 85-145, of which nucleotides 97-104 are replaced with GAAA tetraloop and nucleotides 134-137 are replaced with GAAA tetraloop receptor.
VV: U4 small nuclear RNA variant: Native sequence 85-145, of which nucleotides 97-104 are replaced with GAAA tetraloop and nucleotides 134-137 are replaced with GAAA tetraloop receptor.
XX: U4 small nuclear RNA variant: Native sequence 85-145, of which nucleotides 97-104 are replaced with GAAA tetraloop and nucleotides 134-137 are replaced with GAAA tetraloop receptor.
YY: U4 small nuclear RNA variant: Native sequence 85-145, of which nucleotides 97-104 are replaced with GAAA tetraloop and nucleotides 134-137 are replaced with GAAA tetraloop receptor.
VVV: U4 small nuclear RNA variant: Native sequence 85-145, of which nucleotides 97-104 are replaced with GAAA tetraloop and nucleotides 134-137 are replaced with GAAA tetraloop receptor.
XXX: U4 small nuclear RNA variant: Native sequence 85-145, of which nucleotides 97-104 are replaced with GAAA tetraloop and nucleotides 134-137 are replaced with GAAA tetraloop receptor.
YYY: U4 small nuclear RNA variant: Native sequence 85-145, of which nucleotides 97-104 are replaced with GAAA tetraloop and nucleotides 134-137 are replaced with GAAA tetraloop receptor.
VVVV: U4 small nuclear RNA variant: Native sequence 85-145, of which nucleotides 97-104 are replaced with GAAA tetraloop and nucleotides 134-137 are replaced with GAAA tetraloop receptor.
XXXX: U4 small nuclear RNA variant: Native sequence 85-145, of which nucleotides 97-104 are replaced with GAAA tetraloop and nucleotides 134-137 are replaced with GAAA tetraloop receptor.
YYYY: U4 small nuclear RNA variant: Native sequence 85-145, of which nucleotides 97-104 are replaced with GAAA tetraloop and nucleotides 134-137 are replaced with GAAA tetraloop receptor.


分子量 (理論値)分子数
合計 (水以外)1,229,00896
ポリマ－1,229,00896
非ポリマー00
水543
1
A: Small nuclear ribonucleoprotein Sm D3
B: Small nuclear ribonucleoprotein-associated proteins B and B'
C: Small nuclear ribonucleoprotein Sm D1
D: Small nuclear ribonucleoprotein Sm D2
F: Small nuclear ribonucleoprotein F
E: Small nuclear ribonucleoprotein E
G: Small nuclear ribonucleoprotein G
V: U4 small nuclear RNA variant: Native sequence 85-145, of which nucleotides 97-104 are replaced with GAAA tetraloop and nucleotides 134-137 are replaced with GAAA tetraloop receptor.


分子量 (理論値)分子数
合計 (水以外)102,4178
ポリマ－102,4178
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
2
H: Small nuclear ribonucleoprotein Sm D3
I: Small nuclear ribonucleoprotein-associated proteins B and B'
J: Small nuclear ribonucleoprotein Sm D1
K: Small nuclear ribonucleoprotein Sm D2
M: Small nuclear ribonucleoprotein F
L: Small nuclear ribonucleoprotein E
N: Small nuclear ribonucleoprotein G
X: U4 small nuclear RNA variant: Native sequence 85-145, of which nucleotides 97-104 are replaced with GAAA tetraloop and nucleotides 134-137 are replaced with GAAA tetraloop receptor.


分子量 (理論値)分子数
合計 (水以外)102,4178
ポリマ－102,4178
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
3
O: Small nuclear ribonucleoprotein Sm D3
P: Small nuclear ribonucleoprotein-associated proteins B and B'
Q: Small nuclear ribonucleoprotein Sm D1
R: Small nuclear ribonucleoprotein Sm D2
T: Small nuclear ribonucleoprotein F
S: Small nuclear ribonucleoprotein E
U: Small nuclear ribonucleoprotein G
Y: U4 small nuclear RNA variant: Native sequence 85-145, of which nucleotides 97-104 are replaced with GAAA tetraloop and nucleotides 134-137 are replaced with GAAA tetraloop receptor.


分子量 (理論値)分子数
合計 (水以外)102,4178
ポリマ－102,4178
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
4
AA: Small nuclear ribonucleoprotein Sm D3
BB: Small nuclear ribonucleoprotein-associated proteins B and B'
CC: Small nuclear ribonucleoprotein Sm D1
DD: Small nuclear ribonucleoprotein Sm D2
FF: Small nuclear ribonucleoprotein F
EE: Small nuclear ribonucleoprotein E
GG: Small nuclear ribonucleoprotein G
VV: U4 small nuclear RNA variant: Native sequence 85-145, of which nucleotides 97-104 are replaced with GAAA tetraloop and nucleotides 134-137 are replaced with GAAA tetraloop receptor.


分子量 (理論値)分子数
合計 (水以外)102,4178
ポリマ－102,4178
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
5
HH: Small nuclear ribonucleoprotein Sm D3
II: Small nuclear ribonucleoprotein-associated proteins B and B'
JJ: Small nuclear ribonucleoprotein Sm D1
KK: Small nuclear ribonucleoprotein Sm D2
MM: Small nuclear ribonucleoprotein F
LL: Small nuclear ribonucleoprotein E
NN: Small nuclear ribonucleoprotein G
XX: U4 small nuclear RNA variant: Native sequence 85-145, of which nucleotides 97-104 are replaced with GAAA tetraloop and nucleotides 134-137 are replaced with GAAA tetraloop receptor.


分子量 (理論値)分子数
合計 (水以外)102,4178
ポリマ－102,4178
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
6
OO: Small nuclear ribonucleoprotein Sm D3
PP: Small nuclear ribonucleoprotein-associated proteins B and B'
QQ: Small nuclear ribonucleoprotein Sm D1
RR: Small nuclear ribonucleoprotein Sm D2
TT: Small nuclear ribonucleoprotein F
SS: Small nuclear ribonucleoprotein E
UU: Small nuclear ribonucleoprotein G
YY: U4 small nuclear RNA variant: Native sequence 85-145, of which nucleotides 97-104 are replaced with GAAA tetraloop and nucleotides 134-137 are replaced with GAAA tetraloop receptor.


分子量 (理論値)分子数
合計 (水以外)102,4178
ポリマ－102,4178
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
7
AAA: Small nuclear ribonucleoprotein Sm D3
BBB: Small nuclear ribonucleoprotein-associated proteins B and B'
CCC: Small nuclear ribonucleoprotein Sm D1
DDD: Small nuclear ribonucleoprotein Sm D2
FFF: Small nuclear ribonucleoprotein F
EEE: Small nuclear ribonucleoprotein E
GGG: Small nuclear ribonucleoprotein G
VVV: U4 small nuclear RNA variant: Native sequence 85-145, of which nucleotides 97-104 are replaced with GAAA tetraloop and nucleotides 134-137 are replaced with GAAA tetraloop receptor.


分子量 (理論値)分子数
合計 (水以外)102,4178
ポリマ－102,4178
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
8
HHH: Small nuclear ribonucleoprotein Sm D3
III: Small nuclear ribonucleoprotein-associated proteins B and B'
JJJ: Small nuclear ribonucleoprotein Sm D1
KKK: Small nuclear ribonucleoprotein Sm D2
MMM: Small nuclear ribonucleoprotein F
LLL: Small nuclear ribonucleoprotein E
NNN: Small nuclear ribonucleoprotein G
XXX: U4 small nuclear RNA variant: Native sequence 85-145, of which nucleotides 97-104 are replaced with GAAA tetraloop and nucleotides 134-137 are replaced with GAAA tetraloop receptor.


分子量 (理論値)分子数
合計 (水以外)102,4178
ポリマ－102,4178
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
9
OOO: Small nuclear ribonucleoprotein Sm D3
PPP: Small nuclear ribonucleoprotein-associated proteins B and B'
QQQ: Small nuclear ribonucleoprotein Sm D1
RRR: Small nuclear ribonucleoprotein Sm D2
TTT: Small nuclear ribonucleoprotein F
SSS: Small nuclear ribonucleoprotein E
UUU: Small nuclear ribonucleoprotein G
YYY: U4 small nuclear RNA variant: Native sequence 85-145, of which nucleotides 97-104 are replaced with GAAA tetraloop and nucleotides 134-137 are replaced with GAAA tetraloop receptor.


分子量 (理論値)分子数
合計 (水以外)102,4178
ポリマ－102,4178
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
10
AAAA: Small nuclear ribonucleoprotein Sm D3
BBBB: Small nuclear ribonucleoprotein-associated proteins B and B'
CCCC: Small nuclear ribonucleoprotein Sm D1
DDDD: Small nuclear ribonucleoprotein Sm D2
FFFF: Small nuclear ribonucleoprotein F
EEEE: Small nuclear ribonucleoprotein E
GGGG: Small nuclear ribonucleoprotein G
VVVV: U4 small nuclear RNA variant: Native sequence 85-145, of which nucleotides 97-104 are replaced with GAAA tetraloop and nucleotides 134-137 are replaced with GAAA tetraloop receptor.


分子量 (理論値)分子数
合計 (水以外)102,4178
ポリマ－102,4178
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
11
HHHH: Small nuclear ribonucleoprotein Sm D3
IIII: Small nuclear ribonucleoprotein-associated proteins B and B'
JJJJ: Small nuclear ribonucleoprotein Sm D1
KKKK: Small nuclear ribonucleoprotein Sm D2
MMMM: Small nuclear ribonucleoprotein F
LLLL: Small nuclear ribonucleoprotein E
NNNN: Small nuclear ribonucleoprotein G
XXXX: U4 small nuclear RNA variant: Native sequence 85-145, of which nucleotides 97-104 are replaced with GAAA tetraloop and nucleotides 134-137 are replaced with GAAA tetraloop receptor.


分子量 (理論値)分子数
合計 (水以外)102,4178
ポリマ－102,4178
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
12
OOOO: Small nuclear ribonucleoprotein Sm D3
PPPP: Small nuclear ribonucleoprotein-associated proteins B and B'
QQQQ: Small nuclear ribonucleoprotein Sm D1
RRRR: Small nuclear ribonucleoprotein Sm D2
TTTT: Small nuclear ribonucleoprotein F
SSSS: Small nuclear ribonucleoprotein E
UUUU: Small nuclear ribonucleoprotein G
YYYY: U4 small nuclear RNA variant: Native sequence 85-145, of which nucleotides 97-104 are replaced with GAAA tetraloop and nucleotides 134-137 are replaced with GAAA tetraloop receptor.


分子量 (理論値)分子数
合計 (水以外)102,4178
ポリマ－102,4178
非ポリマー00
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)248.010, 248.010, 251.940
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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要素

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Small nuclear ribonucleoprotein ... , 6種, 72分子 AHOAAHHOOAAAHHHOOOAAAAHHHHOOOOCJQCCJJQQCCCJJJQQQCCCCJJJJQQQQDKRDDKKRR...

#1: タンパク質
Small nuclear ribonucleoprotein Sm D3 / Sm-D3 / snRNP core protein D3


分子量: 13783.114 Da / 分子数: 12 / 由来タイプ: 組換発現 / 詳細: engineered, co-expressed with SM B / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: SNRPD3 / プラスミド: PQE30 / 詳細 (発現宿主): co-expressed with Sm B / 発現宿主: Escherichia coli K-12 (大腸菌) / 株 (発現宿主): K-12 / Variant (発現宿主): SG13009 PREP4 / 参照: UniProt: P62318
#3: タンパク質
Small nuclear ribonucleoprotein Sm D1 / Sm-D1 / Sm-D autoantigen / snRNP core protein D1


分子量: 13153.460 Da / 分子数: 12 / 由来タイプ: 組換発現 / 詳細: engineered, co-expressed with SM D2 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: SNRPD1 / プラスミド: PET / 詳細 (発現宿主): COEXPRESSED WITH SM-D2 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / Variant (発現宿主): PLYSS / 参照: UniProt: P62314
#4: 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: 12 / 由来タイプ: 組換発現 / 詳細: engineered, co-expressed with SM D1 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: SNRPD2 / プラスミド: PET / 詳細 (発現宿主): COEXPRESSED WITH SM-D1 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / Variant (発現宿主): PLYSS / 参照: UniProt: P62316
#5: タンパク質
Small nuclear ribonucleoprotein F / snRNP-F / Sm protein F / SmF


分子量: 9734.171 Da / 分子数: 12 / 由来タイプ: 組換発現 / 詳細: engineered, co-expressed with SM E and SM G / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: SNRPF, PBSCF / プラスミド: PET15B / 詳細 (発現宿主): Co-expressed with Sm E and Sm G / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: P62306
#6: タンパク質
Small nuclear ribonucleoprotein E / snRNP-E / Sm protein E / SmE


分子量: 10817.601 Da / 分子数: 12 / 由来タイプ: 組換発現 / 詳細: engineered, co-expressed with SM F and SM G / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: SNRPE / プラスミド: PET15B / 詳細 (発現宿主): Co-expressed with SmF and Sm G / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: P62304
#7: タンパク質
Small nuclear ribonucleoprotein G / snRNP-G / Sm protein G / SmG


分子量: 8508.084 Da / 分子数: 12 / 由来タイプ: 組換発現 / 詳細: engineered, co-expressed with SM E and SM F / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: SNRPG, PBSCG / プラスミド: PET15B / 詳細 (発現宿主): Co-expressed with SmE and SmF / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: P62308

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タンパク質 / RNA鎖 / 非ポリマー , 3種, 27分子 BIPBBIIPPBBBIIIPPPBBBBIIIIPPPPVXYVVXXYYVVVXXXYYYVVVVXXXXYYYY

#2: タンパク質
Small nuclear ribonucleoprotein-associated proteins B and B' / snRNP-B / Sm protein B/B' / SmB/B'


分子量: 10911.931 Da / 分子数: 12 / 由来タイプ: 組換発現
詳細: engineered; residues 1-95 of sequence expressed, co-expressed with SM D3
由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: SNRPB, COD, SNRPB1 / プラスミド: PQE30 / 詳細 (発現宿主): co-expressed with Sm D3 / 発現宿主: Escherichia coli K-12 (大腸菌) / 株 (発現宿主): K-12 / Variant (発現宿主): SG13009 PREP4 / 参照: UniProt: P14678
#8: RNA鎖
U4 small nuclear RNA variant: Native sequence 85-145, of which nucleotides 97-104 are replaced with GAAA tetraloop and nucleotides 134-137 are replaced with GAAA tetraloop receptor.


分子量: 21957.041 Da / 分子数: 12 / 由来タイプ: 組換発現 / 詳細: IN VITRO TRANSCRIPTION WITH T7 RNA POLYMERASE / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: RNU4-1 / 発現宿主: synthetic construct (人工物)
#9: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 3 / 由来タイプ: 天然 / 式: H2O

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実験情報

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実験

実験手法: X線回折

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試料調製

結晶マシュー密度: 3.6 Å3/Da / 溶媒含有率: 63 % / 解説: hexagonal bipyramid
結晶化温度: 293 K / 手法: 蒸気拡散法, シッティングドロップ法
詳細: 4-10% PEG 550 MME, 0.1M KSCN or (NH4)2SO4, 0.1 M TRIS PH 8.0-8.5 10 MM MGCL2, 2 MM CYCLEN.
PH範囲: 8.0-8.5

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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: SRS / ビームライン: PX9.6 / 波長: 0.9795 Å
検出器タイプ: ADSC QUANTUM 4 / 検出器: CCD / 日付: 2004年7月13日
放射プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 0.9795 Å / 相対比: 1
Reflection twin
タイプCrystal-IDIDOperatorDomain-IDFraction
pseudo-merohedral11H, K, L10.2177
pseudo-merohedral11-K, -H, -L20.2825
pseudo-merohedral11K, H, -L30.2833
pseudo-merohedral11-h,-k,l40.2165
反射解像度: 3.59→66.16 Å / Num. all: 202467 / Num. obs: 202467 / % possible obs: 82.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / 冗長度: 2 % / Rmerge(I) obs: 0.21 / Net I/σ(I): 3.3
反射 シェル解像度: 3.59→3.68 Å / 冗長度: 1.9 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 1.1 / % possible all: 20.8

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解析

ソフトウェア
名称バージョン分類
REFMAC5.8.0073精密化
XDSデータ削減
SCALA6データスケーリング
PHASER2.5.2位相決定
精密化構造決定の手法: 分子置換
開始モデル: 4PJO

4pjo


解像度: 3.6→66.154 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.896 / WRfactor Rfree: 0.205 / WRfactor Rwork: 0.164 / Data cutoff high absF: 0 / Data cutoff low absF: 0.2 / 交差検証法: FREE R-VALUE / σ(F): 0 / ESU R Free: 0.124 / 詳細: Hydrogens have been added in their riding positions
Rfactor反射数%反射Selection details
Rfree0.2238 8251 4.9 %Random selection
Rwork0.1767 158528 --
all0.179 ---
obs0.17899 166779 83.075 %-
溶媒の処理イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.2 Å / 溶媒モデル: MASK BULK SOLVENT
原子変位パラメータBiso mean: 128.369 Å2
Baniso -1Baniso -2Baniso -3
1--5.014 Å2-0 Å2-0 Å2
2---5.014 Å2-0 Å2
3---10.028 Å2
精密化ステップサイクル: LAST / 解像度: 3.6→66.154 Å
タンパク質核酸リガンド溶媒全体
原子数54046 17436 0 3 71485
拘束条件
Refine-IDタイプDev idealDev ideal target数
X-RAY DIFFRACTIONr_bond_refined_d0.010.01774296
X-RAY DIFFRACTIONr_angle_refined_deg1.3991.777104006
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.49156712
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.88524.3432390
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.511510886
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.17315406
X-RAY DIFFRACTIONr_chiral_restr0.0720.211731
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02148130
X-RAY DIFFRACTIONr_nbd_refined0.2370.230582
X-RAY DIFFRACTIONr_nbtor_refined0.3030.248648
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.22310
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3460.2326
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2990.234
X-RAY DIFFRACTIONr_mcbond_it13.2111.53127133
X-RAY DIFFRACTIONr_mcangle_it21.40217.19533750
X-RAY DIFFRACTIONr_scbond_it12.97913.72147163
X-RAY DIFFRACTIONr_scangle_it21.11320.55770256
X-RAY DIFFRACTIONr_lrange_it35.898123.122305545
X-RAY DIFFRACTIONr_ncsr_local_group_10.0140.05103
X-RAY DIFFRACTIONr_ncsr_local_group_20.0240.05101
X-RAY DIFFRACTIONr_ncsr_local_group_30.0580.05103
X-RAY DIFFRACTIONr_ncsr_local_group_40.0040.05102
X-RAY DIFFRACTIONr_ncsr_local_group_50.0040.05102
X-RAY DIFFRACTIONr_ncsr_local_group_60.0080.05103
X-RAY DIFFRACTIONr_ncsr_local_group_70.0040.05101
X-RAY DIFFRACTIONr_ncsr_local_group_80.0040.05100
X-RAY DIFFRACTIONr_ncsr_local_group_90.0120.05103
X-RAY DIFFRACTIONr_ncsr_local_group_100.0050.05102
X-RAY DIFFRACTIONr_ncsr_local_group_110.0050.05102
X-RAY DIFFRACTIONr_ncsr_local_group_120.0110.0591
X-RAY DIFFRACTIONr_ncsr_local_group_130.0060.0590
X-RAY DIFFRACTIONr_ncsr_local_group_140.0060.0590
X-RAY DIFFRACTIONr_ncsr_local_group_150.040.0591
X-RAY DIFFRACTIONr_ncsr_local_group_160.0080.0590
X-RAY DIFFRACTIONr_ncsr_local_group_170.0060.0590
X-RAY DIFFRACTIONr_ncsr_local_group_180.0060.0590
X-RAY DIFFRACTIONr_ncsr_local_group_190.0060.0590
X-RAY DIFFRACTIONr_ncsr_local_group_200.0080.0590
X-RAY DIFFRACTIONr_ncsr_local_group_210.060.0592
X-RAY DIFFRACTIONr_ncsr_local_group_220.0080.0591
X-RAY DIFFRACTIONr_ncsr_local_group_230.0060.05102
X-RAY DIFFRACTIONr_ncsr_local_group_240.0060.05101
X-RAY DIFFRACTIONr_ncsr_local_group_250.0060.05102
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X-RAY DIFFRACTIONr_ncsr_local_group_270.0050.05102
X-RAY DIFFRACTIONr_ncsr_local_group_280.0040.05102
X-RAY DIFFRACTIONr_ncsr_local_group_290.0050.05102
X-RAY DIFFRACTIONr_ncsr_local_group_300.0050.05101
X-RAY DIFFRACTIONr_ncsr_local_group_310.0050.05102
X-RAY DIFFRACTIONr_ncsr_local_group_320.0050.05102
X-RAY DIFFRACTIONr_ncsr_local_group_330.0050.05102
X-RAY DIFFRACTIONr_ncsr_local_group_340.0070.05124
X-RAY DIFFRACTIONr_ncsr_local_group_350.0080.05126
X-RAY DIFFRACTIONr_ncsr_local_group_360.0430.05124
X-RAY DIFFRACTIONr_ncsr_local_group_370.0070.05126
X-RAY DIFFRACTIONr_ncsr_local_group_380.0080.05126
X-RAY DIFFRACTIONr_ncsr_local_group_390.0060.05126
X-RAY DIFFRACTIONr_ncsr_local_group_400.0050.05124
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X-RAY DIFFRACTIONr_ncsr_local_group_420.0090.05126
X-RAY DIFFRACTIONr_ncsr_local_group_430.0320.05124
X-RAY DIFFRACTIONr_ncsr_local_group_440.0070.05126
X-RAY DIFFRACTIONr_ncsr_local_group_450.0120.0586
X-RAY DIFFRACTIONr_ncsr_local_group_460.0130.0586
X-RAY DIFFRACTIONr_ncsr_local_group_470.0120.0586
X-RAY DIFFRACTIONr_ncsr_local_group_480.0130.0586
X-RAY DIFFRACTIONr_ncsr_local_group_490.1060.0586
X-RAY DIFFRACTIONr_ncsr_local_group_500.0130.0587
X-RAY DIFFRACTIONr_ncsr_local_group_510.0130.0586
X-RAY DIFFRACTIONr_ncsr_local_group_520.0120.0586
X-RAY DIFFRACTIONr_ncsr_local_group_530.0070.0586
X-RAY DIFFRACTIONr_ncsr_local_group_540.0070.0585
X-RAY DIFFRACTIONr_ncsr_local_group_550.010.0586
X-RAY DIFFRACTIONr_ncsr_local_group_560.0050.05106
X-RAY DIFFRACTIONr_ncsr_local_group_570.0090.05106
X-RAY DIFFRACTIONr_ncsr_local_group_580.0050.05106
X-RAY DIFFRACTIONr_ncsr_local_group_590.0060.05106
X-RAY DIFFRACTIONr_ncsr_local_group_600.0080.05106
X-RAY DIFFRACTIONr_ncsr_local_group_610.0050.05106
X-RAY DIFFRACTIONr_ncsr_local_group_620.0080.05106
X-RAY DIFFRACTIONr_ncsr_local_group_630.0080.05106
X-RAY DIFFRACTIONr_ncsr_local_group_640.0070.05106
X-RAY DIFFRACTIONr_ncsr_local_group_650.0460.05101
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X-RAY DIFFRACTIONr_ncsr_local_group_680.0050.0587
X-RAY DIFFRACTIONr_ncsr_local_group_690.0060.0586
X-RAY DIFFRACTIONr_ncsr_local_group_700.0050.0587
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X-RAY DIFFRACTIONr_ncsr_local_group_720.0040.0587
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X-RAY DIFFRACTIONr_ncsr_local_group_740.0050.0587
X-RAY DIFFRACTIONr_ncsr_local_group_750.0050.0587
X-RAY DIFFRACTIONr_ncsr_local_group_760.0040.0587
X-RAY DIFFRACTIONr_ncsr_local_group_770.0040.0587
X-RAY DIFFRACTIONr_ncsr_local_group_780.0330.05102
X-RAY DIFFRACTIONr_ncsr_local_group_790.0040.05101
X-RAY DIFFRACTIONr_ncsr_local_group_800.0610.05104
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X-RAY DIFFRACTIONr_ncsr_local_group_870.0070.05102
X-RAY DIFFRACTIONr_ncsr_local_group_880.0070.0589
X-RAY DIFFRACTIONr_ncsr_local_group_890.010.0589
X-RAY DIFFRACTIONr_ncsr_local_group_900.0070.0590
X-RAY DIFFRACTIONr_ncsr_local_group_910.0070.0589
X-RAY DIFFRACTIONr_ncsr_local_group_920.0070.0589
X-RAY DIFFRACTIONr_ncsr_local_group_930.0070.0589
X-RAY DIFFRACTIONr_ncsr_local_group_940.0070.0589
X-RAY DIFFRACTIONr_ncsr_local_group_950.0060.0590
X-RAY DIFFRACTIONr_ncsr_local_group_960.010.0590
X-RAY DIFFRACTIONr_ncsr_local_group_970.0060.0589
X-RAY DIFFRACTIONr_ncsr_local_group_980.0050.05103
X-RAY DIFFRACTIONr_ncsr_local_group_990.0050.05104
X-RAY DIFFRACTIONr_ncsr_local_group_1000.0080.05103
X-RAY DIFFRACTIONr_ncsr_local_group_1010.0060.05104
X-RAY DIFFRACTIONr_ncsr_local_group_1020.0060.05104
X-RAY DIFFRACTIONr_ncsr_local_group_1030.0050.05104
X-RAY DIFFRACTIONr_ncsr_local_group_1040.0040.05103
X-RAY DIFFRACTIONr_ncsr_local_group_1050.0060.05103
X-RAY DIFFRACTIONr_ncsr_local_group_1060.0050.05104
X-RAY DIFFRACTIONr_ncsr_local_group_1070.0050.05104
X-RAY DIFFRACTIONr_ncsr_local_group_1080.0090.05125
X-RAY DIFFRACTIONr_ncsr_local_group_1090.0430.05123
X-RAY DIFFRACTIONr_ncsr_local_group_1100.0090.05125
X-RAY DIFFRACTIONr_ncsr_local_group_1110.0090.05125
X-RAY DIFFRACTIONr_ncsr_local_group_1120.0080.05125
X-RAY DIFFRACTIONr_ncsr_local_group_1130.0160.05125
X-RAY DIFFRACTIONr_ncsr_local_group_1140.0080.05125
X-RAY DIFFRACTIONr_ncsr_local_group_1150.010.05125
X-RAY DIFFRACTIONr_ncsr_local_group_1160.010.05124
X-RAY DIFFRACTIONr_ncsr_local_group_1170.0090.05125
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X-RAY DIFFRACTIONr_ncsr_local_group_1190.0450.0587
X-RAY DIFFRACTIONr_ncsr_local_group_1200.0730.0591
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X-RAY DIFFRACTIONr_ncsr_local_group_1220.0070.0586
X-RAY DIFFRACTIONr_ncsr_local_group_1230.0850.0589
X-RAY DIFFRACTIONr_ncsr_local_group_1240.020.0588
X-RAY DIFFRACTIONr_ncsr_local_group_1250.0730.0586
X-RAY DIFFRACTIONr_ncsr_local_group_1260.1120.0588
X-RAY DIFFRACTIONr_ncsr_local_group_1270.0510.0587
X-RAY DIFFRACTIONr_ncsr_local_group_1280.0090.05106
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X-RAY DIFFRACTIONr_ncsr_local_group_1300.0050.05106
X-RAY DIFFRACTIONr_ncsr_local_group_1310.0080.05106
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X-RAY DIFFRACTIONr_ncsr_local_group_1390.0060.0586
X-RAY DIFFRACTIONr_ncsr_local_group_1400.0060.0587
X-RAY DIFFRACTIONr_ncsr_local_group_1410.0060.0587
X-RAY DIFFRACTIONr_ncsr_local_group_1420.0060.0587
X-RAY DIFFRACTIONr_ncsr_local_group_1430.0060.0587
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X-RAY DIFFRACTIONr_ncsr_local_group_1500.0050.05100
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X-RAY DIFFRACTIONr_ncsr_local_group_1940.0090.05106
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X-RAY DIFFRACTIONr_ncsr_local_group_4180.0070.0587
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X-RAY DIFFRACTIONr_ncsr_local_group_4200.0070.0587
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X-RAY DIFFRACTIONr_ncsr_local_group_4330.0050.0585
X-RAY DIFFRACTIONr_ncsr_local_group_4340.1150.0587
X-RAY DIFFRACTIONr_ncsr_local_group_4350.0070.0586
X-RAY DIFFRACTIONr_ncsr_local_group_4360.0090.05106
X-RAY DIFFRACTIONr_ncsr_local_group_4370.0450.05101
X-RAY DIFFRACTIONr_ncsr_local_group_4380.0080.05106
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X-RAY DIFFRACTIONr_ncsr_local_group_4410.0040.0587
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X-RAY DIFFRACTIONr_ncsr_local_group_4440.0070.0590
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X-RAY DIFFRACTIONr_ncsr_local_group_4470.0060.05103
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X-RAY DIFFRACTIONr_ncsr_local_group_4490.0080.05128
X-RAY DIFFRACTIONr_ncsr_local_group_4500.0080.0585
X-RAY DIFFRACTIONr_ncsr_local_group_4510.0070.0585
X-RAY DIFFRACTIONr_ncsr_local_group_4520.0470.05101
X-RAY DIFFRACTIONr_ncsr_local_group_4530.0070.05106
X-RAY DIFFRACTIONr_ncsr_local_group_4540.0060.0587
X-RAY DIFFRACTIONr_ncsr_local_group_4550.0050.0587
X-RAY DIFFRACTIONr_ncsr_local_group_4560.0040.05102
X-RAY DIFFRACTIONr_ncsr_local_group_4570.0430.0590
X-RAY DIFFRACTIONr_ncsr_local_group_4580.0050.05104
X-RAY DIFFRACTIONr_ncsr_local_group_4590.0330.05125
X-RAY DIFFRACTIONr_ncsr_local_group_4600.0070.0585
X-RAY DIFFRACTIONr_ncsr_local_group_4610.0460.05101
X-RAY DIFFRACTIONr_ncsr_local_group_4620.0050.0587
X-RAY DIFFRACTIONr_ncsr_local_group_4630.1040.05659
X-RAY DIFFRACTIONr_ncsr_local_group_4640.1090.05659
X-RAY DIFFRACTIONr_ncsr_local_group_4650.1090.05656
X-RAY DIFFRACTIONr_ncsr_local_group_4660.1160.05654
X-RAY DIFFRACTIONr_ncsr_local_group_4670.1080.05656
X-RAY DIFFRACTIONr_ncsr_local_group_4680.1010.05657
X-RAY DIFFRACTIONr_ncsr_local_group_4690.1080.05657
X-RAY DIFFRACTIONr_ncsr_local_group_4700.1110.05657
X-RAY DIFFRACTIONr_ncsr_local_group_4710.1060.05647
X-RAY DIFFRACTIONr_ncsr_local_group_4720.1210.05659
X-RAY DIFFRACTIONr_ncsr_local_group_4730.1080.05657
X-RAY DIFFRACTIONr_ncsr_local_group_4740.080.05667
X-RAY DIFFRACTIONr_ncsr_local_group_4750.0940.05657
X-RAY DIFFRACTIONr_ncsr_local_group_4760.0940.05664
X-RAY DIFFRACTIONr_ncsr_local_group_4770.080.05660
X-RAY DIFFRACTIONr_ncsr_local_group_4780.0690.05660
X-RAY DIFFRACTIONr_ncsr_local_group_4790.0790.05661
X-RAY DIFFRACTIONr_ncsr_local_group_4800.0830.05664
X-RAY DIFFRACTIONr_ncsr_local_group_4810.0910.05654
X-RAY DIFFRACTIONr_ncsr_local_group_4820.0960.05662
X-RAY DIFFRACTIONr_ncsr_local_group_4830.0830.05671
X-RAY DIFFRACTIONr_ncsr_local_group_4840.0640.05669
X-RAY DIFFRACTIONr_ncsr_local_group_4850.0690.05659
X-RAY DIFFRACTIONr_ncsr_local_group_4860.0550.05665
X-RAY DIFFRACTIONr_ncsr_local_group_4870.0590.05666
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X-RAY DIFFRACTIONr_ncsr_local_group_4890.0580.05670
X-RAY DIFFRACTIONr_ncsr_local_group_4900.0960.05656
X-RAY DIFFRACTIONr_ncsr_local_group_4910.0790.05671
X-RAY DIFFRACTIONr_ncsr_local_group_4920.0540.05671
X-RAY DIFFRACTIONr_ncsr_local_group_4930.0890.05660
X-RAY DIFFRACTIONr_ncsr_local_group_4940.0730.05661
X-RAY DIFFRACTIONr_ncsr_local_group_4950.070.05661
X-RAY DIFFRACTIONr_ncsr_local_group_4960.0640.05667
X-RAY DIFFRACTIONr_ncsr_local_group_4970.0750.05664
X-RAY DIFFRACTIONr_ncsr_local_group_4980.0980.05658
X-RAY DIFFRACTIONr_ncsr_local_group_4990.090.05663
X-RAY DIFFRACTIONr_ncsr_local_group_5000.0850.05672
X-RAY DIFFRACTIONr_ncsr_local_group_5010.0770.05658
X-RAY DIFFRACTIONr_ncsr_local_group_5020.0750.05662
X-RAY DIFFRACTIONr_ncsr_local_group_5030.0720.05659
X-RAY DIFFRACTIONr_ncsr_local_group_5040.0750.05661
X-RAY DIFFRACTIONr_ncsr_local_group_5050.1090.05647
X-RAY DIFFRACTIONr_ncsr_local_group_5060.0930.05654
X-RAY DIFFRACTIONr_ncsr_local_group_5070.0760.05664
X-RAY DIFFRACTIONr_ncsr_local_group_5080.0530.05674
X-RAY DIFFRACTIONr_ncsr_local_group_5090.0450.05672
X-RAY DIFFRACTIONr_ncsr_local_group_5100.0480.05675
X-RAY DIFFRACTIONr_ncsr_local_group_5110.0930.05653
X-RAY DIFFRACTIONr_ncsr_local_group_5120.0880.05661
X-RAY DIFFRACTIONr_ncsr_local_group_5130.050.05671
X-RAY DIFFRACTIONr_ncsr_local_group_5140.0570.05666
X-RAY DIFFRACTIONr_ncsr_local_group_5150.0570.05670
X-RAY DIFFRACTIONr_ncsr_local_group_5160.0950.05653
X-RAY DIFFRACTIONr_ncsr_local_group_5170.0920.05660
X-RAY DIFFRACTIONr_ncsr_local_group_5180.0650.05671
X-RAY DIFFRACTIONr_ncsr_local_group_5190.0520.05673
X-RAY DIFFRACTIONr_ncsr_local_group_5200.0930.05654
X-RAY DIFFRACTIONr_ncsr_local_group_5210.0820.05665
X-RAY DIFFRACTIONr_ncsr_local_group_5220.0520.05668
X-RAY DIFFRACTIONr_ncsr_local_group_5230.1020.05655
X-RAY DIFFRACTIONr_ncsr_local_group_5240.080.05666
X-RAY DIFFRACTIONr_ncsr_local_group_5250.0630.05671
X-RAY DIFFRACTIONr_ncsr_local_group_5260.1080.05653
X-RAY DIFFRACTIONr_ncsr_local_group_5270.1040.05655
X-RAY DIFFRACTIONr_ncsr_local_group_5280.0890.05665
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.6-3.6930.2521520.2330861481921.8503
3.693-3.7940.2752320.22545641445133.188
3.794-3.9040.2492840.21665061402148.4274
3.904-4.0230.2544830.201100491366677.0672
4.023-4.1550.276180.195125931324799.7282
4.155-4.30.2496080.185120631271899.6304
4.3-4.4620.2146110.17116671232599.6187
4.462-4.6430.1936320.161112341193799.4052
4.643-4.8480.2346160.16107431144099.292
4.848-5.0840.2025360.147102001083499.0954
5.084-5.3570.2244910.16497821039898.7978
5.357-5.680.2424780.1739166978698.549
5.68-6.0690.2554190.1918648922898.2553
6.069-6.550.2234720.1987942859897.86
6.55-7.1680.2644180.1977239785997.4297
7.168-8.0030.2553310.1816633719296.8298
8.003-9.2180.2042970.1735778631096.2757
9.218-11.2360.2022800.1494821535095.3458
11.236-15.6650.1471780.143748417294.1035
15.665-66.1720.1711150.2162066240690.6484

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万見について

-
お知らせ

-
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

-
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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