4PKD | pdb_00004pkd

U1-70k in complex with U1 snRNA stem-loops 1 and U1-A RRM in complex with stem-loop 2

PDB DOI: https://doi.org/10.2210/pdb4PKD/pdb
NAKB: 4PKD

Classification: GENE REGULATION
Organism(s): Homo sapiens, Sus scrofa
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2014-05-14 Released: 2014-12-31
Deposition Author(s): Oubridge, C., Kondo, Y., van Roon, A.M., Nagai, K.
Funding Organization(s): Nakajima Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.258 (Depositor), 0.255 (DCC)
R-Value Work:
0.197 (Depositor), 0.201 (DCC)
R-Value Observed:
0.200 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

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.

(2015) Elife 4

PubMed: 25555158 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.7554/eLife.04986
Primary Citation Related Structures:
4PJO, 4PKD

PubMed Abstract:
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.

Organizational Affiliation

Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom.

Macromolecule Content

Total Structure Weight: 50.11 kDa
Atom Count: 3,252
Modeled Residue Count: 295
Deposited Residue Count: 334
Unique protein chains: 1
Unique nucleic acid chains: 1

Macromolecules

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
U1 small nuclear ribonucleoprotein A,U1 small nuclear ribonucleoprotein 70 kDa	B	279	Sus scrofa, Homo sapiens This entity is chimeric	Mutation(s): 1 Gene Names: SNRPA, SNRNP70, RNPU1Z, RPU1, SNRP70, U1AP1
UniProt & NIH Common Fund Data Resources
Find proteins for P08621 (Homo sapiens) Explore P08621 Go to UniProtKB: P08621
PHAROS: P08621 GTEx: ENSG00000104852
Find proteins for Q06AA4 (Sus scrofa) Explore Q06AA4 Go to UniProtKB: Q06AA4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Groups	P08621 Q06AA4
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 1
U1 snRNA stem-loops 1 and 2 (55-MER)	A [auth V]	55	Homo sapiens
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IMD Query on IMD Download:Ideal Coordinates CCD File SDF format, chain F [auth B] MOL2 format, chain F [auth B] mmCIF format, chain F [auth B]	F [auth B]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain F [auth B] Interactions & Density Focus chain F [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain D [auth V] SDF format, chain C [auth V] MOL2 format, chain E [auth B] MOL2 format, chain D [auth V] MOL2 format, chain C [auth V] mmCIF format, chain E [auth B] mmCIF format, chain D [auth V] mmCIF format, chain C [auth V]	C [auth V], D [auth V], E [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth V] Focus chain D [auth V] Focus chain E [auth B] Interactions & Density Focus chain C [auth V] Focus chain D [auth V] Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.258 (Depositor), 0.255 (DCC)
R-Value Work: 0.197 (Depositor), 0.201 (DCC)
R-Value Observed: 0.200 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.22	α = 90
b = 66.6	β = 110.95
c = 93.73	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2014-12-31

Deposition Author(s):

Funding Organization	Location	Grant Number
Nakajima Foundation	Japan	--

Revision History (Full details and data files)

Version 1.0: 2014-12-31
Type: Initial release
Version 1.1: 2015-01-14
Changes: Database references
Version 1.2: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Refinement description