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- PDB-3pgw: Crystal structure of human U1 snRNP -

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Basic information

Entry
Database: PDB / ID: 3pgw
TitleCrystal structure of human U1 snRNP
Components
  • DNA 5'-D(*AP*GP*GP*TP*AP*AP*GP*TP*A)-3'
  • Sm B
  • Sm G
  • Sm-D1
  • Sm-D2
  • Sm-D3
  • Sm-E
  • Sm-F
  • U1 snRNAU1 spliceosomal RNA
  • U1-70K
  • U1-A
Keywordssplicing/DNA/RNA / PROTEIN-RNA COMPLEX / U1 snRNA / Sm fold / Sm core / RRM / Splicing / mRNA / snRNPs / splicing factors / splicing-DNA-RNA complex
Function / homology
Function and homology information


negative regulation of protein refolding / histone mRNA metabolic process / regulation of ATP-dependent activity / 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 ...negative regulation of protein refolding / histone mRNA metabolic process / regulation of ATP-dependent activity / 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 / import into nucleus / protein methylation / U12-type spliceosomal complex / methylosome / 7-methylguanosine cap hypermethylation / U1 snRNP binding / pICln-Sm protein complex / spliceosomal tri-snRNP complex / small nuclear ribonucleoprotein complex / P granule / SMN-Sm protein complex / U2-type spliceosomal complex / negative regulation of chaperone-mediated autophagy / telomerase RNA binding / U2-type precatalytic spliceosome / positive regulation of mRNA splicing, via spliceosome / telomerase holoenzyme complex / U2-type prespliceosome assembly / U2-type catalytic step 2 spliceosome / commitment complex / U4 snRNP / U2 snRNP / RNA Polymerase II Transcription Termination / U1 snRNP / U2-type prespliceosome / precatalytic spliceosome / termination of RNA polymerase II transcription / spliceosomal complex assembly / mRNA Splicing - Minor Pathway / regulation of RNA splicing / U5 snRNP / spliceosomal snRNP assembly / U1 snRNA binding / 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 / nuclear speck / ribonucleoprotein complex / mRNA binding / enzyme binding / DNA binding / RNA binding / extracellular exosome / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
snRNP70, RNA recognition motif / U1 small nuclear ribonucleoprotein of 70kDa N-terminal / U1 small nuclear ribonucleoprotein of 70kDa MW N terminal / U1 small nuclear ribonucleoprotein A, RNA recognition motif 2 / U1 small nuclear ribonucleoprotein A, RNA recognition motif 1 / Small ribonucleoprotein associated, SmB/SmN / Small nuclear ribonucleoprotein D1 / Small nuclear ribonucleoprotein Sm D3 / Small nuclear ribonucleoprotein Sm D2 / Small nuclear ribonucleoprotein E ...snRNP70, RNA recognition motif / U1 small nuclear ribonucleoprotein of 70kDa N-terminal / U1 small nuclear ribonucleoprotein of 70kDa MW N terminal / U1 small nuclear ribonucleoprotein A, RNA recognition motif 2 / U1 small nuclear ribonucleoprotein A, RNA recognition motif 1 / 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 / Sm-like protein Lsm7/SmG / Like-Sm (LSM) domain containing protein, LSm4/SmD1/SmD3 / Sm-like protein Lsm6/SmF / LSM domain / LSM domain, eukaryotic/archaea-type / snRNP Sm proteins / : / Sm domain profile. / LSM domain superfamily / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
DNA / RNA / RNA (> 10) / RNA (> 100) / Small nuclear ribonucleoprotein G / U1 small nuclear ribonucleoprotein 70 kDa / U1 small nuclear ribonucleoprotein A / Small nuclear ribonucleoprotein-associated proteins B and B' / Small nuclear ribonucleoprotein E / Small nuclear ribonucleoprotein F ...DNA / RNA / RNA (> 10) / RNA (> 100) / Small nuclear ribonucleoprotein G / U1 small nuclear ribonucleoprotein 70 kDa / U1 small nuclear ribonucleoprotein A / 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 / Small nuclear ribonucleoprotein-associated protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement, MIRAS / Resolution: 4.4 Å
AuthorsWeber, G. / Trowitzsch, S. / Kastner, B. / Luehrmann, R. / Wahl, M.C.
CitationJournal: Embo J. / Year: 2010
Title: Functional organization of the Sm core in the crystal structure of human U1 snRNP.
Authors: Weber, G. / Trowitzsch, S. / Kastner, B. / Luhrmann, R. / Wahl, M.C.
History
DepositionNov 2, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 29, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: U1-A
S: U1-70K
Z: Sm-D3
B: Sm B
X: Sm-D1
Y: Sm-D2
F: Sm-F
E: Sm-E
G: Sm G
P: U1-A
L: U1-70K
W: Sm-D3
Q: Sm B
U: Sm-D1
V: Sm-D2
I: Sm-F
H: Sm-E
J: Sm G
R: U1 snRNA
N: U1 snRNA
D: DNA 5'-D(*AP*GP*GP*TP*AP*AP*GP*TP*A)-3'
M: DNA 5'-D(*AP*GP*GP*TP*AP*AP*GP*TP*A)-3'


Theoretical massNumber of molelcules
Total (without water)464,10522
Polymers464,10522
Non-polymers00
Water0
1
A: U1-A
S: U1-70K
Z: Sm-D3
B: Sm B
X: Sm-D1
Y: Sm-D2
F: Sm-F
E: Sm-E
G: Sm G
R: U1 snRNA
D: DNA 5'-D(*AP*GP*GP*TP*AP*AP*GP*TP*A)-3'


Theoretical massNumber of molelcules
Total (without water)232,05211
Polymers232,05211
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
P: U1-A
L: U1-70K
W: Sm-D3
Q: Sm B
U: Sm-D1
V: Sm-D2
I: Sm-F
H: Sm-E
J: Sm G
N: U1 snRNA
M: DNA 5'-D(*AP*GP*GP*TP*AP*AP*GP*TP*A)-3'


Theoretical massNumber of molelcules
Total (without water)232,05211
Polymers232,05211
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)358.420, 88.220, 150.900
Angle α, β, γ (deg.)90.00, 111.88, 90.00
Int Tables number5
Space group name H-MC121
Detailsbiological assembly 1: chains A, S, Z, B, X, Y, F, E, G, R, D / biological assembly 2: chains P, L ,W, Q, U, V, I, H, J, N, M

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Components

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Protein , 9 types, 18 molecules APSLZWBQXUYVFIEHGJ

#1: Protein U1-A / U1 snRNP A / U1 small nuclear ribonucleoprotein A / U1A / Coordinate model: Cα atoms only


Mass: 31319.533 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA / References: UniProt: P09012
#2: Protein U1-70K / U1 snRNP 70 kDa / snRNP70 / U1 small nuclear ribonucleoprotein 70 kDa / Coordinate model: Cα atoms only


Mass: 51683.184 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA / References: UniProt: P08621
#3: Protein Sm-D3 / Small nuclear ribonucleoprotein Sm D3 / snRNP core protein D3 / Coordinate model: Cα atoms only


Mass: 13940.308 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA / References: UniProt: P62318
#4: Protein Sm B / Small nuclear ribonucleoprotein polypeptides B and B1 / Coordinate model: Cα atoms only


Mass: 23686.004 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA / References: UniProt: Q66K91, UniProt: P14678*PLUS
#5: Protein Sm-D1 / Small nuclear ribonucleoprotein Sm D1 / Sm-D autoantigen / snRNP core protein D1 / Coordinate model: Cα atoms only


Mass: 13310.653 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA / References: UniProt: P62314
#6: Protein Sm-D2 / Small nuclear ribonucleoprotein Sm D2 / snRNP core protein D2 / Coordinate model: Cα atoms only


Mass: 13551.928 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA / References: UniProt: P62316
#7: Protein Sm-F / snRNP-F / Sm protein F / Small nuclear ribonucleoprotein F / SmF / Coordinate model: Cα atoms only


Mass: 9734.171 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA / References: UniProt: P62306
#8: Protein Sm-E / snRNP-E / Sm protein E / Small nuclear ribonucleoprotein E / SmE / Coordinate model: Cα atoms only


Mass: 10817.601 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA / References: UniProt: P62304
#9: Protein Sm G / Small nuclear ribonucleoprotein polypeptide G / isoform CRA_a / Coordinate model: Cα atoms only


Mass: 8508.084 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA / References: UniProt: D6W5G6, UniProt: P62308*PLUS

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RNA chain / DNA chain , 2 types, 4 molecules RNDM

#10: RNA chain U1 snRNA / U1 spliceosomal RNA / Coordinate model: P atoms only


Mass: 52697.070 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA
#11: DNA chain DNA 5'-D(*AP*GP*GP*TP*AP*AP*GP*TP*A)-3' / Coordinate model: P atoms only


Mass: 2803.873 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: DNA oligonucleotide

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.43 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 8-10% PEG 4000, 0.1 M Trisodium citrate, 2 mM EDTA, 100 mM NaCl, 1-2% Anapoe X-305, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.999 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 30, 2007
RadiationMonochromator: LN2 cooled fixed-exit Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 4.4→100 Å / Num. all: 28274 / Num. obs: 28079 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2
Reflection shellResolution: 4.4→4.6 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 2 / Num. unique all: 3480 / Rsym value: 0.73 / % possible all: 99.3

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Processing

Software
NameVersionClassification
gclientdata collection
MAR345data collection
RemDAqdata collection
PHASERphasing
SHARPphasing
PHENIXrefinement
CNS1.3refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: molecular replacement, MIRAS / Resolution: 4.4→100 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.348 1403 RANDOM
Rwork0.299 --
all-28077 -
obs-28077 -
Refinement stepCycle: LAST / Resolution: 4.4→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1716 342 0 0 2058
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.004
X-RAY DIFFRACTIONf_angle_deg1.201

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