[English] 日本語
Yorodumi
- PDB-5yzg: The Cryo-EM Structure of Human Catalytic Step I Spliceosome (C co... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 5yzg
TitleThe Cryo-EM Structure of Human Catalytic Step I Spliceosome (C complex) at 4.1 angstrom resolution
Components
  • (Peptidyl-prolyl cis-trans isomerase ...Prolyl isomerase) x 2
  • (Pre-mRNA-processing factor ...) x 2
  • (Pre-mRNA-splicing factor ...) x 8
  • (Small nuclear ribonucleoprotein ...SnRNP) x 6
  • (U2 small nuclear ribonucleoprotein ...) x 2
  • (U5 small nuclear ribonucleoprotein ...) x 2
  • 116 kDa U5 small nuclear ribonucleoprotein component
  • Cell division cycle 5-like protein
  • Coiled-coil domain-containing protein 94
  • Crooked neck-like protein 1
  • Eukaryotic initiation factor 4A-III
  • Intron-binding protein aquarius
  • Peptidyl-prolyl cis-trans isomerase-like 1
  • Peptidylprolyl isomerase domain and WD repeat-containing protein 1
  • Pleiotropic regulator 1
  • Pre-mRNA-processing-splicing factor 8
  • Pre-mRNAPrimary transcript
  • Protein BUD31 homolog
  • Protein CASC3
  • Protein mago nashi homolog 2
  • RNA-binding protein 8A
  • SNW domain-containing protein 1
  • Serine/arginine repetitive matrix protein 2
  • Small nuclear ribonucleoprotein-associated proteins B and B'
  • Spliceosome-associated protein CWC15 homolog
  • U2 snRNAU2 spliceosomal RNA
  • U5 snRNAU5 spliceosomal RNA
  • U6 snRNAU6 spliceosomal RNA
  • UNKNOW
KeywordsSPLICING / Structure of a Human Catalytic Step I Spliceosome
Function / homologyLeucine-rich repeat / Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding / Pre-mRNA splicing factor / PRP8 domain IV core / Pre-mRNA splicing factor component Cdc5p/Cef1 / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Ribosomal protein S5 domain 2-type fold / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Tetratricopeptide repeat ...Leucine-rich repeat / Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding / Pre-mRNA splicing factor / PRP8 domain IV core / Pre-mRNA splicing factor component Cdc5p/Cef1 / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Ribosomal protein S5 domain 2-type fold / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Tetratricopeptide repeat / RNA recognition motif, spliceosomal PrP8 / Pre-mRNA-processing-splicing factor 8, U6-snRNA-binding / Spt5 C-terminal domain / CBF1-interacting co-repressor CIR, N-terminal domain / Btz domain / BUD31/G10-related, conserved site / WD40-repeat-containing domain / Myb domain / SKI-interacting protein, SKIP / Small ribonucleoprotein associated, SmB/SmN / Sm-like protein Lsm6/SmF / Peptidyl-prolyl cis-trans isomerase E / Armadillo-type fold / Cyclophilin-type peptidyl-prolyl cis-trans isomerase / CWF11 family / WD40/YVTN repeat-like-containing domain superfamily / RBM8, RNA recognition motif / C2 domain superfamily / 116kDa U5 small nuclear ribonucleoprotein component, C-terminal / EF-G domain III/V-like / U2 small nuclear ribonucleoprotein B'', RNA recognition motif 1 / U2 small nuclear ribonucleoprotein B'', RNA recognition motif 2 / Peptidyl-prolyl cis-trans isomerase E, RNA recognition motif / Small nuclear ribonucleoprotein D1 / Small nuclear ribonucleoprotein F / Small nuclear ribonucleoprotein Sm D3 / Small nuclear ribonucleoprotein G / Pre-mRNA-processing factor 17 / Small nuclear ribonucleoprotein E / Leucine-rich repeat domain superfamily / Intron-binding protein aquarius, N-terminal / 116kDa U5 small nuclear ribonucleoprotein component, N-terminal / Helix hairpin bin domain superfamily / Cyclophilin-like domain superfamily / Protein CASC3 / Pre-mRNA-processing-splicing factor 8 / P-loop containing nucleoside triphosphate hydrolase / Small nuclear ribonucleoprotein Sm D2 / Like-Sm (LSM) domain containing protein, LSm4/SmD1/SmD3 / MIF4G-like domain superfamily / Myb-like transcription factor / WD40-repeat-containing domain superfamily / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / Small GTP-binding protein domain / Sec63 domain / Translation elongation factor EFTu-like, domain 2 / Mago nashi protein / SKI-interacting protein SKIP, SNW domain / Initiation factor eIF-4 gamma, MA3 / MIF4G-like, type 3 / U box domain / U2A'/phosphoprotein 32 family A, C-terminal / HAT (Half-A-TPR) repeat / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / Pre-mRNA-splicing factor Cwf15/Cwc15 / G10 protein / WD40 repeat / Leucine-rich repeat / LSM domain, eukaryotic/archaea-type / SANT/Myb domain / Transcription factor, GTP-binding domain / Ricin B, lectin domain / Elongation factor EFG, domain V-like / ATP-dependent RNA helicase DEAD-box, conserved site / Zinc finger, CCCH-type / Translation elongation factor EFG/EF2, domain IV / Helicase-associated domain / Immunoglobulin E-set / PROCN domain / Ribosomal protein S5 domain 2-type fold, subgroup / RNA helicase, DEAD-box type, Q motif / Helicase superfamily 1/2, ATP-binding domain / Pre-mRNA-splicing factor 19 / mRNA splicing factor SYF2 / mRNA splicing factor Cwf21 domain / Zinc finger, RING/FYVE/PHD-type / Tetratricopeptide repeat-containing domain / PROCT domain / Nucleotide-binding alpha-beta plait domain superfamily / PRO8NT domain / CWC16 protein / Ribonuclease H-like superfamily / Tetratricopeptide-like helical domain superfamily / Domain of unknown function DUF1605 / DEAD/DEAH box helicase domain / LSM domain superfamily / Pre-mRNA-splicing factor Isy1 / Homeobox-like domain superfamily / Translation protein, beta-barrel domain superfamily / Pre-mRNA-splicing factor SPF27
Function and homology information
Specimen sourceHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 4.1 Å resolution
AuthorsZhan, X. / Yan, C. / Zhang, X. / Lei, J. / Shi, Y.
CitationJournal: Science / Year: 2018
Title: Structure of a human catalytic step I spliceosome.
Authors: Xiechao Zhan / Chuangye Yan / Xiaofeng Zhang / Jianlin Lei / Yigong Shi
Abstract: Splicing by the spliceosome involves branching and exon ligation. The branching reaction leads to the formation of the catalytic step I spliceosome (C complex). Here we report the cryo-electron ...Splicing by the spliceosome involves branching and exon ligation. The branching reaction leads to the formation of the catalytic step I spliceosome (C complex). Here we report the cryo-electron microscopy structure of the human C complex at an average resolution of 4.1 angstroms. Compared with the C complex, the human complex contains 11 additional proteins. The step I splicing factors CCDC49 and CCDC94 (Cwc25 and Yju2 in , respectively) closely interact with the DEAH-family adenosine triphosphatase/helicase Prp16 and bridge the gap between Prp16 and the active-site RNA elements. These features, together with structural comparison of the human C and C* complexes, provide mechanistic insights into ribonucleoprotein remodeling and allow the proposition of a working mechanism for the C-to-C* transition.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Dec 14, 2017 / Release: Aug 8, 2018

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-6864
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-6864
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Pre-mRNA-processing-splicing factor 8
B: U5 snRNA
C: 116 kDa U5 small nuclear ribonucleoprotein component
D: U5 small nuclear ribonucleoprotein 200 kDa helicase
E: U5 small nuclear ribonucleoprotein 40 kDa protein
F: U6 snRNA
G: Pre-mRNA
H: U2 snRNA
I: Pre-mRNA-splicing factor SYF1
J: Crooked neck-like protein 1
K: Pre-mRNA-splicing factor SPF27
L: Cell division cycle 5-like protein
y: Pre-mRNA-splicing factor ISY1 homolog
M: Pre-mRNA-splicing factor SYF2
N: Protein BUD31 homolog
O: Pre-mRNA-splicing factor RBM22
P: Spliceosome-associated protein CWC15 homolog
R: SNW domain-containing protein 1
S: Peptidyl-prolyl cis-trans isomerase-like 1
T: Pleiotropic regulator 1
Q: Intron-binding protein aquarius
U: Serine/arginine repetitive matrix protein 2
V: Pre-mRNA-splicing factor CWC22 homolog
W: Pre-mRNA-processing factor 17
X: Pre-mRNA-splicing factor CWC25 homolog
Y: Coiled-coil domain-containing protein 94
Z: Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16
q: Pre-mRNA-processing factor 19
r: Pre-mRNA-processing factor 19
s: Pre-mRNA-processing factor 19
t: Pre-mRNA-processing factor 19
u: Eukaryotic initiation factor 4A-III
v: Protein mago nashi homolog 2
w: RNA-binding protein 8A
x: Protein CASC3
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: U2 small nuclear ribonucleoprotein A'
p: U2 small nuclear ribonucleoprotein B''
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
1: Peptidyl-prolyl cis-trans isomerase E
2: Peptidylprolyl isomerase domain and WD repeat-containing protein 1
3: Peptidyl-prolyl cis-trans isomerase G
4: UNKNOW
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,193,81574
Polyers3,190,64355
Non-polymers3,17319
Water0
1


  • idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

+
Protein/peptide , 19 types, 20 molecules ACJLNPRSTQUYuvwxib24

#1: Protein/peptide Pre-mRNA-processing-splicing factor 8 / 220 kDa U5 snRNP-specific protein / PRP8 homolog / Splicing factor Prp8 / p220


Mass: 273974.250 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q6P2Q9
#3: Protein/peptide 116 kDa U5 small nuclear ribonucleoprotein component / Elongation factor Tu GTP-binding domain-containing protein 2 / SNU114 homolog / hSNU114 / U5 snRNP-specific protein / 116 kDa / U5-116 kDa


Mass: 109560.625 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q15029
#10: Protein/peptide Crooked neck-like protein 1 / Crooked neck homolog / hCrn


Mass: 100610.008 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BZJ0
#12: Protein/peptide Cell division cycle 5-like protein / Cdc5-like protein / Pombe cdc5-related protein


Mass: 92406.883 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q99459
#15: Protein/peptide Protein BUD31 homolog / Protein EDG-2 / Protein G10 homolog


Mass: 17032.850 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: P41223
#17: Protein/peptide Spliceosome-associated protein CWC15 homolog


Mass: 26674.447 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q9P013
#18: Protein/peptide SNW domain-containing protein 1 / Nuclear protein SkiP / Nuclear receptor coactivator NCoA-62 / Ski-interacting protein


Mass: 61770.648 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q13573
#19: Protein/peptide Peptidyl-prolyl cis-trans isomerase-like 1 / PPIase / Rotamase PPIL1


Mass: 18257.805 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y3C6, peptidylprolyl isomerase
#20: Protein/peptide Pleiotropic regulator 1


Mass: 57280.758 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: O43660
#21: Protein/peptide Intron-binding protein aquarius / Intron-binding protein of 160 kDa / IBP160


Mass: 171502.453 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: O60306
#22: Protein/peptide Serine/arginine repetitive matrix protein 2 / 300 kDa nuclear matrix antigen / Serine/arginine-rich splicing factor-related nuclear matrix protein of 300 kDa / Ser/Arg-related nuclear matrix protein of 300 kDa / Splicing coactivator subunit SRm300 / Tax-responsive enhancer element-binding protein 803 / TaxREB803


Mass: 300255.312 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q9UQ35
#26: Protein/peptide Coiled-coil domain-containing protein 94


Mass: 37141.816 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BW85
#29: Protein/peptide Eukaryotic initiation factor 4A-III / eIF4A-III / ATP-dependent RNA helicase DDX48 / ATP-dependent RNA helicase eIF4A-3 / DEAD box protein 48 / Eukaryotic initiation factor 4A-like NUK-34 / Eukaryotic translation initiation factor 4A isoform 3 / Nuclear matrix protein 265 / hNMP 265


Mass: 46930.961 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: P38919, RNA helicase
#30: Protein/peptide Protein mago nashi homolog 2


Mass: 17301.799 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q96A72
#31: Protein/peptide RNA-binding protein 8A / Binder of OVCA1-1 / BOV-1 / RNA-binding motif protein 8A / RNA-binding protein Y14 / Ribonucleoprotein RBM8A


Mass: 19925.070 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y5S9
#32: Protein/peptide Protein CASC3 / Cancer susceptibility candidate gene 3 protein / Metastatic lymph node gene 51 protein / MLN 51 / Protein barentsz / Btz


Mass: 76381.992 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: O15234
#34: Protein/peptide Small nuclear ribonucleoprotein-associated proteins B and B' / snRNP-B / Sm protein B/B' / SmB/B'


Mass: 23459.688 Da / Num. of mol.: 2 / Source: (natural) Homo sapiens (human) / References: UniProt: P14678
#43: Protein/peptide Peptidylprolyl isomerase domain and WD repeat-containing protein 1 / Spliceosome-associated cyclophilin


Mass: 73679.891 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q96BP3, peptidylprolyl isomerase
#45: Protein/peptide UNKNOW


Mass: 2631.853 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human)

+
RNA chain , 4 types, 4 molecules BFGH

#2: RNA chain U5 snRNA / U5 spliceosomal RNA


Mass: 37254.855 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human)
#6: RNA chain U6 snRNA / U6 spliceosomal RNA


Mass: 34404.438 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human)
#7: RNA chain Pre-mRNA / Primary transcript


Mass: 88088.820 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human)
#8: RNA chain U2 snRNA / U2 spliceosomal RNA


Mass: 60186.445 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human)

+
U5 small nuclear ribonucleoprotein ... , 2 types, 2 molecules DE

#4: Protein/peptide U5 small nuclear ribonucleoprotein 200 kDa helicase / Activating signal cointegrator 1 complex subunit 3-like 1 / BRR2 homolog / U5 snRNP-specific 200 kDa protein / U5-200KD


Mass: 244823.422 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: O75643, RNA helicase
#5: Protein/peptide U5 small nuclear ribonucleoprotein 40 kDa protein / U5-40K / 38 kDa-splicing factor / Prp8-binding protein / hPRP8BP / U5 snRNP-specific 40 kDa protein / WD repeat-containing protein 57


Mass: 39359.492 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q96DI7

+
Pre-mRNA-splicing factor ... , 8 types, 8 molecules IKyMOVXZ

#9: Protein/peptide Pre-mRNA-splicing factor SYF1 / Protein HCNP / XPA-binding protein 2


Mass: 100148.711 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q9HCS7
#11: Protein/peptide Pre-mRNA-splicing factor SPF27 / Breast carcinoma-amplified sequence 2 / DNA amplified in mammary carcinoma 1 protein / Spliceosome-associated protein SPF 27


Mass: 26163.420 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: O75934
#13: Protein/peptide Pre-mRNA-splicing factor ISY1 homolog


Mass: 35499.074 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q9ULR0
#14: Protein/peptide Pre-mRNA-splicing factor SYF2 / CCNDBP1-interactor / p29


Mass: 28780.518 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: O95926
#16: Protein/peptide Pre-mRNA-splicing factor RBM22 / RNA-binding motif protein 22 / Zinc finger CCCH domain-containing protein 16


Mass: 46959.555 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NW64
#23: Protein/peptide Pre-mRNA-splicing factor CWC22 homolog / Nucampholin homolog / fSAPb


Mass: 105646.578 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q9HCG8
#25: Protein/peptide Pre-mRNA-splicing factor CWC25 homolog / Coiled-coil domain-containing protein 49 / Spliceosome-associated protein homolog CWC25


Mass: 49736.820 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NXE8
#27: Protein/peptide Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16 / ATP-dependent RNA helicase DHX38 / DEAH box protein 38


Mass: 140720.641 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q92620, RNA helicase

+
Pre-mRNA-processing factor ... , 2 types, 5 molecules Wqrst

#24: Protein/peptide Pre-mRNA-processing factor 17 / Cell division cycle 40 homolog / EH-binding protein 3 / Ehb3 / PRP17 homolog / hPRP17


Mass: 65612.180 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: O60508
#28: Protein/peptide
Pre-mRNA-processing factor 19 / Nuclear matrix protein 200 / PRP19/PSO4 homolog / hPso4 / RING-type E3 ubiquitin transferase PRP19 / Senescence evasion factor


Mass: 55245.547 Da / Num. of mol.: 4 / Source: (natural) Homo sapiens (human)
References: UniProt: Q9UMS4, RING-type E3 ubiquitin transferase

+
Small nuclear ribonucleoprotein ... , 6 types, 12 molecules hajckdmfleng

#33: Protein/peptide Small nuclear ribonucleoprotein Sm D3 / Sm-D3 / snRNP core protein D3


Mass: 13940.308 Da / Num. of mol.: 2 / Source: (natural) Homo sapiens (human) / References: UniProt: P62318
#35: Protein/peptide Small nuclear ribonucleoprotein Sm D1 / Sm-D1 / Sm-D autoantigen / snRNP core protein D1


Mass: 13310.653 Da / Num. of mol.: 2 / Source: (natural) Homo sapiens (human) / References: UniProt: P62314
#36: Protein/peptide Small nuclear ribonucleoprotein Sm D2 / Sm-D2 / snRNP core protein D2


Mass: 13551.928 Da / Num. of mol.: 2 / Source: (natural) Homo sapiens (human) / References: UniProt: P62316
#37: Protein/peptide Small nuclear ribonucleoprotein F / snRNP-F / Sm protein F / SmF


Mass: 9734.171 Da / Num. of mol.: 2 / Source: (natural) Homo sapiens (human) / References: UniProt: P62306
#38: Protein/peptide Small nuclear ribonucleoprotein E / snRNP-E / Sm protein E / SmE


Mass: 10817.601 Da / Num. of mol.: 2 / Source: (natural) Homo sapiens (human) / References: UniProt: P62304
#39: Protein/peptide Small nuclear ribonucleoprotein G / snRNP-G / Sm protein G / SmG


Mass: 8508.084 Da / Num. of mol.: 2 / Source: (natural) Homo sapiens (human) / References: UniProt: P62308

+
U2 small nuclear ribonucleoprotein ... , 2 types, 2 molecules op

#40: Protein/peptide U2 small nuclear ribonucleoprotein A' / U2 snRNP A'


Mass: 28456.584 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: P09661
#41: Protein/peptide U2 small nuclear ribonucleoprotein B'' / U2 snRNP B''


Mass: 25524.367 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: P08579

+
Peptidyl-prolyl cis-trans isomerase ... , 2 types, 2 molecules 13

#42: Protein/peptide Peptidyl-prolyl cis-trans isomerase E / PPIase E / Cyclophilin E / Cyclophilin-33 / Rotamase E


Mass: 33475.773 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q9UNP9, peptidylprolyl isomerase
#44: Protein/peptide Peptidyl-prolyl cis-trans isomerase G / Peptidyl-prolyl isomerase G / CASP10 / Clk-associating RS-cyclophilin / SRcyp / Cyclophilin G / Rotamase G


Mass: 88854.336 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q13427, peptidylprolyl isomerase

+
Non-polymers , 6 types, 19 molecules

#46: Chemical ChemComp-I6P / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE


Mass: 660.035 Da / Num. of mol.: 1 / Formula: C6H18O24P6 / Phytic acid
#47: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Formula: C10H16N5O14P3 / Guanosine triphosphate / Comment: GTP (energy-carrying molecule) *YM
#48: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Formula: Mg / Magnesium
#49: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Formula: C10H15N5O10P2 / Adenosine diphosphate / Comment: ADP (energy-carrying molecule) *YM
#50: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Formula: Zn / Zinc
#51: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Formula: C10H16N5O13P3 / Adenosine triphosphate / Comment: ATP (energy-carrying molecule) *YM

+
Details

Sequence detailsThe N (unknown nucleotide) between G-1 and G1 is added intentionally to fill in the cleavage by RNA splicing.

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Human Catalytic Step I Spliceosome / Type: COMPLEX
Entity ID: 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45
Source: NATURAL
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.9
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

-
Processing

SoftwareName: REFMAC / Version: 5.8.0069 / Classification: refinement
EM software
IDNameVersionCategory
4Gctf0.66CTF correction
10RELION2.0initial Euler assignment
11RELION2.0final Euler assignment
12RELION2.0classification
13RELION2.03D reconstruction
CTF correctionType: NONE
Particle selectionNumber of particles selected: 1464033
SymmetryPoint symmetry: C1
3D reconstructionResolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 53633 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Least-squares processHighest resolution: 4.1 Å
Number of atoms included #1Total: 55623
Refine LS restraints
Refine IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0160.01857399
ELECTRON MICROSCOPYr_bond_other_d0.0030.02050656
ELECTRON MICROSCOPYr_angle_refined_deg1.8831.87079000
ELECTRON MICROSCOPYr_angle_other_deg1.0423.000116696
ELECTRON MICROSCOPYr_dihedral_angle_1_deg7.6015.0006170
ELECTRON MICROSCOPYr_dihedral_angle_2_deg34.31623.5502341
ELECTRON MICROSCOPYr_dihedral_angle_3_deg18.47115.0008765
ELECTRON MICROSCOPYr_dihedral_angle_4_deg21.04015.000382
ELECTRON MICROSCOPYr_chiral_restr0.0980.2008624
ELECTRON MICROSCOPYr_gen_planes_refined0.0090.02160078
ELECTRON MICROSCOPYr_gen_planes_other0.0030.02013269
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it15.03615.56924872
ELECTRON MICROSCOPYr_mcbond_other15.03515.56924871
ELECTRON MICROSCOPYr_mcangle_it24.89023.26430978
ELECTRON MICROSCOPYr_mcangle_other24.89023.26430979
ELECTRON MICROSCOPYr_scbond_it17.71717.27632527
ELECTRON MICROSCOPYr_scbond_other17.71717.27732528
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other30.19725.38148023
ELECTRON MICROSCOPYr_long_range_B_refined47.913240216
ELECTRON MICROSCOPYr_long_range_B_other47.913240217
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
Refine LS shellHighest resolution: 4.1 Å / R factor R work: 0.542 / Lowest resolution: 4.206 Å / Number reflection R free: 0 / Number reflection R work: 31339 / Total number of bins used: 20 / Percent reflection obs: 1

+
About Yorodumi

-
News

-
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.: Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator

External links: EMDB at EBI / Contact to PDBj

-
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more