4PJO | pdb_00004pjo

Minimal U1 snRNP

PDB DOI: https://doi.org/10.2210/pdb4PJO/pdb
NAKB: 4PJO

Classification: SPLICING
Organism(s): Homo sapiens
Expression System: Escherichia coli, Escherichia coli BL21(DE3), Escherichia coli B
Mutation(s): No

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.30 Å
R-Value Free:
0.255 (Depositor), 0.188 (DCC)
R-Value Work:
0.207 (Depositor)
R-Value Observed:
0.209 (Depositor)

Starting Model: experimental
View more details

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: 453.82 kDa
Atom Count: 26,921
Modeled Residue Count: 2,947
Deposited Residue Count: 3,456
Unique protein chains: 9
Unique nucleic acid chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Small nuclear ribonucleoprotein Sm D3	A, HA [auth o], L [auth a], W [auth O]	126	Homo sapiens	Mutation(s): 0 Gene Names: SNRPD3
UniProt & NIH Common Fund Data Resources
Find proteins for P62318 (Homo sapiens) Explore P62318 Go to UniProtKB: P62318
PHAROS: P62318 GTEx: ENSG00000100028
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62318
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Small nuclear ribonucleoprotein-associated proteins B and B'	B, IA [auth p], M [auth b], X [auth P]	95	Homo sapiens	Mutation(s): 0 Gene Names: SNRPB, COD, SNRPB1
UniProt & NIH Common Fund Data Resources
Find proteins for P14678 (Homo sapiens) Explore P14678 Go to UniProtKB: P14678
PHAROS: P14678 GTEx: ENSG00000125835
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P14678
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Small nuclear ribonucleoprotein Sm D1	C, JA [auth q], N [auth c], Y [auth Q]	91	Homo sapiens	Mutation(s): 0 Gene Names: SNRPD1
UniProt & NIH Common Fund Data Resources
Find proteins for P62314 (Homo sapiens) Explore P62314 Go to UniProtKB: P62314
PHAROS: P62314 GTEx: ENSG00000167088
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62314
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Small nuclear ribonucleoprotein Sm D2	D, KA [auth r], O [auth d], Z [auth R]	118	Homo sapiens	Mutation(s): 0 Gene Names: SNRPD2
UniProt & NIH Common Fund Data Resources
Find proteins for P62316 (Homo sapiens) Explore P62316 Go to UniProtKB: P62316
PHAROS: P62316 GTEx: ENSG00000125743
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62316
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Small nuclear ribonucleoprotein E	AA [auth S], E, LA [auth s], P [auth e]	92	Homo sapiens	Mutation(s): 0 Gene Names: SNRPE
UniProt & NIH Common Fund Data Resources
Find proteins for P62304 (Homo sapiens) Explore P62304 Go to UniProtKB: P62304
PHAROS: P62304 GTEx: ENSG00000182004
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62304
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Small nuclear ribonucleoprotein F	BA [auth T], F, MA [auth t], Q [auth f]	75	Homo sapiens	Mutation(s): 0 Gene Names: SNRPF, PBSCF
UniProt & NIH Common Fund Data Resources
Find proteins for P62306 (Homo sapiens) Explore P62306 Go to UniProtKB: P62306
PHAROS: P62306 GTEx: ENSG00000139343
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62306
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Small nuclear ribonucleoprotein G	CA [auth U], G, NA [auth u], R [auth g]	76	Homo sapiens	Mutation(s): 0 Gene Names: SNRPG, PBSCG
UniProt & NIH Common Fund Data Resources
Find proteins for P62308 (Homo sapiens) Explore P62308 Go to UniProtKB: P62308
PHAROS: P62308 GTEx: ENSG00000143977
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62308
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
U1 small nuclear ribonucleoprotein 70 kDa	DA [auth N], H [auth K], OA [auth n], S [auth k]	60	Homo sapiens	Mutation(s): 0 Gene Names: 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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P08621
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
U1 small nuclear ribonucleoprotein C	EA [auth M], I [auth L], PA [auth m], T [auth l]	61	Homo sapiens	Mutation(s): 0 Gene Names: SNRPC
UniProt & NIH Common Fund Data Resources
Find proteins for P09234 (Homo sapiens) Explore P09234 Go to UniProtKB: P09234
PHAROS: P09234 GTEx: ENSG00000124562
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P09234
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 10
U1 RNA variant (48-MER) with 4-helix junction replaced by kissing loop (HIV-1 (Mal) DIS) and shorter stem-loop 4.	FA [auth 3], J [auth 1], QA [auth 4], U [auth 2]	60	Homo sapiens
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism
Entity ID: 11
RNA (5'-R(APGPGPUPAPAPGPUPCPC)-3')	GA [auth Y], K [auth X], RA [auth y], V [auth x]	10	Homo sapiens
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EPE Query on EPE Download:Ideal Coordinates CCD File SDF format, chain HB [auth 2] SDF format, chain TA [auth 1] MOL2 format, chain HB [auth 2] MOL2 format, chain TA [auth 1] mmCIF format, chain HB [auth 2] mmCIF format, chain TA [auth 1]	HB [auth 2], TA [auth 1]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain HB [auth 2] Focus chain TA [auth 1]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain AC [auth y] MOL2 format, chain AC [auth y] mmCIF format, chain AC [auth y]	AC [auth y]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AC [auth y]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain FB [auth l] SDF format, chain NB [auth M] SDF format, chain SA [auth L] SDF format, chain UB [auth m] MOL2 format, chain FB [auth l] MOL2 format, chain NB [auth M] MOL2 format, chain SA [auth L] MOL2 format, chain UB [auth m] mmCIF format, chain FB [auth l] mmCIF format, chain NB [auth M] mmCIF format, chain SA [auth L] mmCIF format, chain UB [auth m]	FB [auth l], NB [auth M], SA [auth L], UB [auth m]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain FB [auth l] Focus chain NB [auth M] Focus chain SA [auth L] Focus chain UB [auth m]
EOH Query on EOH Download:Ideal Coordinates CCD File SDF format, chain VB [auth 4] MOL2 format, chain VB [auth 4] mmCIF format, chain VB [auth 4]	VB [auth 4]	ETHANOL C₂ H₆ O LFQSCWFLJHTTHZ-UHFFFAOYSA-N		Interactions Focus chain VB [auth 4]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain CB [auth 1] SDF format, chain DB [auth b] SDF format, chain EB [auth b] SDF format, chain MB [auth Q] SDF format, chain SB [auth 3] SDF format, chain TB [auth 3] MOL2 format, chain CB [auth 1] MOL2 format, chain DB [auth b] MOL2 format, chain EB [auth b] MOL2 format, chain MB [auth Q] MOL2 format, chain SB [auth 3] MOL2 format, chain TB [auth 3] mmCIF format, chain CB [auth 1] mmCIF format, chain DB [auth b] mmCIF format, chain EB [auth b] mmCIF format, chain MB [auth Q] mmCIF format, chain SB [auth 3] mmCIF format, chain TB [auth 3]	CB [auth 1] DB [auth b] EB [auth b] MB [auth Q] SB [auth 3] CB [auth 1], DB [auth b], EB [auth b], MB [auth Q], SB [auth 3], TB [auth 3]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain CB [auth 1] Focus chain DB [auth b] Focus chain EB [auth b] Focus chain MB [auth Q] Focus chain SB [auth 3] Focus chain TB [auth 3]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain XB [auth 4] MOL2 format, chain XB [auth 4] mmCIF format, chain XB [auth 4]	XB [auth 4]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain XB [auth 4]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain AB [auth 1] SDF format, chain BB [auth 1] SDF format, chain GB [auth l] SDF format, chain IB [auth 2] SDF format, chain JB [auth 2] SDF format, chain KB [auth 2] SDF format, chain LB [auth 2] SDF format, chain OB [auth 3] SDF format, chain PB [auth 3] SDF format, chain QB [auth 3] SDF format, chain RB [auth 3] SDF format, chain UA [auth 1] SDF format, chain VA [auth 1] SDF format, chain WA [auth 1] SDF format, chain WB [auth 4] SDF format, chain XA [auth 1] SDF format, chain YA [auth 1] SDF format, chain YB [auth y] SDF format, chain ZA [auth 1] SDF format, chain ZB [auth y] MOL2 format, chain AB [auth 1] MOL2 format, chain BB [auth 1] MOL2 format, chain GB [auth l] MOL2 format, chain IB [auth 2] MOL2 format, chain JB [auth 2] MOL2 format, chain KB [auth 2] MOL2 format, chain LB [auth 2] MOL2 format, chain OB [auth 3] MOL2 format, chain PB [auth 3] MOL2 format, chain QB [auth 3] MOL2 format, chain RB [auth 3] MOL2 format, chain UA [auth 1] MOL2 format, chain VA [auth 1] MOL2 format, chain WA [auth 1] MOL2 format, chain WB [auth 4] MOL2 format, chain XA [auth 1] MOL2 format, chain YA [auth 1] MOL2 format, chain YB [auth y] MOL2 format, chain ZA [auth 1] MOL2 format, chain ZB [auth y] mmCIF format, chain AB [auth 1] mmCIF format, chain BB [auth 1] mmCIF format, chain GB [auth l] mmCIF format, chain IB [auth 2] mmCIF format, chain JB [auth 2] mmCIF format, chain KB [auth 2] mmCIF format, chain LB [auth 2] mmCIF format, chain OB [auth 3] mmCIF format, chain PB [auth 3] mmCIF format, chain QB [auth 3] mmCIF format, chain RB [auth 3] mmCIF format, chain UA [auth 1] mmCIF format, chain VA [auth 1] mmCIF format, chain WA [auth 1] mmCIF format, chain WB [auth 4] mmCIF format, chain XA [auth 1] mmCIF format, chain YA [auth 1] mmCIF format, chain YB [auth y] mmCIF format, chain ZA [auth 1] mmCIF format, chain ZB [auth y]	AB [auth 1] BB [auth 1] GB [auth l] IB [auth 2] JB [auth 2] AB [auth 1], BB [auth 1], GB [auth l], IB [auth 2], JB [auth 2], KB [auth 2], LB [auth 2], OB [auth 3], PB [auth 3], QB [auth 3], RB [auth 3], UA [auth 1], VA [auth 1], WA [auth 1], WB [auth 4], XA [auth 1], YA [auth 1], YB [auth y], ZA [auth 1], ZB [auth y]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AB [auth 1] Focus chain BB [auth 1] Focus chain GB [auth l] Focus chain IB [auth 2] Focus chain JB [auth 2] Focus chain KB [auth 2] Focus chain LB [auth 2] Focus chain OB [auth 3] Focus chain PB [auth 3] Focus chain QB [auth 3] Focus chain RB [auth 3] Focus chain UA [auth 1] Focus chain VA [auth 1] Focus chain WA [auth 1] Focus chain WB [auth 4] Focus chain XA [auth 1] Focus chain YA [auth 1] Focus chain YB [auth y] Focus chain ZA [auth 1] Focus chain ZB [auth y]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.30 Å
R-Value Free: 0.255 (Depositor), 0.188 (DCC)
R-Value Work: 0.207 (Depositor)
R-Value Observed: 0.209 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.359	α = 90
b = 172.627	β = 90
c = 256.322	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing
Coot	model building
REFMAC	refinement

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2014-12-31

Deposition Author(s):

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

4PJO | pdb_00004pjo

Minimal U1 snRNP

Literature

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

Biological Assembly 1

Biological Assembly 2

Biological Assembly 3

Biological Assembly 4

Macromolecules

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 2

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 3

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 4

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 5

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 6

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 7

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 8

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 9

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 10

Sequence Annotations

Entity ID: 11

Sequence Annotations

Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation

Entry History

Deposition Data

Revision History (Full details and data files)