ISDA

Deposition Date 2014-05-12

Release Date 2014-12-31

Last Version Date 2023-12-20

Entry Detail

PDB ID:

4PJO

Keywords:

SPLICING

Title:

Minimal U1 snRNP

Biological Source:

Source Organism:

Homo sapiens (Taxon ID: 9606)

Host Organism:

Escherichia coli

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

3.30 Å

R-Value Free:

0.25

R-Value Work:

0.20

R-Value Observed:

0.20

Space Group:

P 21 21 21

Download Validation Report

Macromolecular Entities

Polymer Type:polyribonucleotide
Molecule:U1 RNA variant (48-MER) with 4-helix junction replaced by kissing loop (HIV-1 (Mal) DIS) and shorter stem-loop 4.
Chain IDs:J (auth: 1), U (auth: 2), FA (auth: 3), QA (auth: 4)
Chain Length:60
Number of Molecules:4
Biological Source:Homo sapiens

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small nuclear ribonucleoprotein Sm D3
Gene (Uniprot):SNRPD3
Chain IDs:A, L (auth: a), W (auth: O), HA (auth: o)
Chain Length:126
Number of Molecules:4
Biological Source:Homo sapiens

UniProt ID:P62318 Pfam ID:PF01423

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small nuclear ribonucleoprotein-associated proteins B and B'
Gene (Uniprot):SNRPB
Chain IDs:B, M (auth: b), X (auth: P), IA (auth: p)
Chain Length:95
Number of Molecules:4
Biological Source:Homo sapiens

UniProt ID:P14678 Pfam ID:PF01423

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small nuclear ribonucleoprotein Sm D1
Gene (Uniprot):SNRPD1
Mutations:M1V
Chain IDs:C, N (auth: c), Y (auth: Q), JA (auth: q)
Chain Length:91
Number of Molecules:4
Biological Source:Homo sapiens

UniProt ID:P62314 Pfam ID:PF01423

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small nuclear ribonucleoprotein Sm D2
Gene (Uniprot):SNRPD2
Chain IDs:D, O (auth: d), Z (auth: R), KA (auth: r)
Chain Length:118
Number of Molecules:4
Biological Source:Homo sapiens

UniProt ID:P62316 Pfam ID:PF01423

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small nuclear ribonucleoprotein E
Gene (Uniprot):SNRPE
Chain IDs:E, P (auth: e), AA (auth: S), LA (auth: s)
Chain Length:92
Number of Molecules:4
Biological Source:Homo sapiens

UniProt ID:P62304 Pfam ID:PF01423

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small nuclear ribonucleoprotein F
Gene (Uniprot):SNRPF
Chain IDs:F, Q (auth: f), BA (auth: T), MA (auth: t)
Chain Length:75
Number of Molecules:4
Biological Source:Homo sapiens

UniProt ID:P62306 Pfam ID:PF01423

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small nuclear ribonucleoprotein G
Gene (Uniprot):SNRPG
Chain IDs:G, R (auth: g), CA (auth: U), NA (auth: u)
Chain Length:76
Number of Molecules:4
Biological Source:Homo sapiens

UniProt ID:P62308 Pfam ID:PF01423

Protein Blast

Polymer Type:polypeptide(L)
Molecule:U1 small nuclear ribonucleoprotein 70 kDa
Gene (Uniprot):SNRNP70
Mutations:M1G
Chain IDs:H (auth: K), S (auth: k), DA (auth: N), OA (auth: n)
Chain Length:60
Number of Molecules:4
Biological Source:Homo sapiens

UniProt ID:P08621 Pfam ID:PF12220

Protein Blast

Polymer Type:polypeptide(L)
Molecule:U1 small nuclear ribonucleoprotein C
Gene (Uniprot):SNRPC
Chain IDs:I (auth: L), T (auth: l), EA (auth: M), PA (auth: m)
Chain Length:61
Number of Molecules:4
Biological Source:Homo sapiens

UniProt ID:P09234 Pfam ID:PF06220

Polymer Type:polyribonucleotide
Molecule:RNA (5'-R(*AP*GP*GP*UP*AP*AP*GP*UP*CP*C)-3')
Chain IDs:K (auth: X), V (auth: x), GA (auth: Y), RA (auth: y)
Chain Length:10
Number of Molecules:4
Biological Source:Homo sapiens

Ligand Molecules

EOH

EPE

SO4

Primary Citation

Crystal structure of human U1 snRNP, a small nuclear ribonucleoprotein particle, reveals the mechanism of 5' splice site recognition.

Kondo, Y, Oubridge, C, van Roon, A.M, Nagai, K.Show

Elife 4 ? ? (2015)

PMID: 25555158 DOI: 10.7554/eLife.04986

Abstact

U1 snRNP binds to the 5' exon-intron junction of pre-mRNA and thus plays a crucial role at an early stage of pre-mRNA splicing. We present two crystal structures of engineered U1 sub-structures, which together reveal at atomic resolution an almost complete network of protein-protein and RNA-protein interactions within U1 snRNP, and show how the 5' splice site of pre-mRNA is recognised by U1 snRNP. The zinc-finger of U1-C interacts with the duplex between pre-mRNA and the 5'-end of U1 snRNA. The binding of the RNA duplex is stabilized by hydrogen bonds and electrostatic interactions between U1-C and the RNA backbone around the splice junction but U1-C makes no base-specific contacts with pre-mRNA. The structure, together with RNA binding assays, shows that the selection of 5'-splice site nucleotides by U1 snRNP is achieved predominantly through basepairing with U1 snRNA whilst U1-C fine-tunes relative affinities of mismatched 5'-splice sites.

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Primary Citation of related structures