2OZB | pdb_00002ozb

Structure of a human Prp31-15.5K-U4 snRNA complex

PDB DOI: https://doi.org/10.2210/pdb2OZB/pdb
NAKB: 2OZB

Classification: RNA BINDING PROTEIN/RNA
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3), Escherichia coli
Mutation(s): No

Deposited: 2007-02-26 Released: 2007-03-20
Deposition Author(s): Liu, S., Luehrmann, R., Wahl, M.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.248 (Depositor), 0.232 (DCC)
R-Value Work:
0.206 (Depositor), 0.195 (DCC)
R-Value Observed:
0.208 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Binding of the human Prp31 Nop domain to a composite RNA-protein platform in U4 snRNP.

Liu, S., Li, P., Dybkov, O., Nottrott, S., Hartmuth, K., Luhrmann, R., Carlomagno, T., Wahl, M.C.

(2007) Science 316: 115-120

PubMed: 17412961 Search on PubMed
DOI: https://doi.org/10.1126/science.1137924
Primary Citation Related Structures:
2OZB

PubMed Abstract:
Although highly homologous, the spliceosomal hPrp31 and the nucleolar Nop56 and Nop58 (Nop56/58) proteins recognize different ribonucleoprotein (RNP) particles. hPrp31 interacts with complexes containing the 15.5K protein and U4 or U4atac small nuclear RNA (snRNA), whereas Nop56/58 associate with 15.5K-box C/D small nucleolar RNA complexes. We present structural and biochemical analyses of hPrp31-15.5K-U4 snRNA complexes that show how the conserved Nop domain in hPrp31 maintains high RNP binding selectivity despite relaxed RNA sequence requirements. The Nop domain is a genuine RNP binding module, exhibiting RNA and protein binding surfaces. Yeast two-hybrid analyses suggest a link between retinitis pigmentosa and an aberrant hPrp31-hPrp6 interaction that blocks U4/U6-U5 tri-snRNP formation.

Organizational Affiliation

Abteilung Zelluläre Biochemie, Max-Planck-Institut für Biophysikalische Chemie, Am Fassberg 11, D-37077 Göttingen, Germany.

Macromolecule Content

Total Structure Weight: 107.81 kDa
Atom Count: 7,375
Modeled Residue Count: 796
Deposited Residue Count: 846
Unique protein chains: 2
Unique nucleic acid chains: 1

Macromolecules

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
U4/U6.U5 tri-snRNP 15.5 kDa protein	C [auth A], E [auth D]	130	Homo sapiens	Mutation(s): 0 Gene Names: NHP2L1
UniProt & NIH Common Fund Data Resources
Find proteins for P55769 (Homo sapiens) Explore P55769 Go to UniProtKB: P55769
PHAROS: P55769 GTEx: ENSG00000100138
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P55769
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
U4/U6 small nuclear ribonucleoprotein Prp31	D [auth B], F [auth E]	260	Homo sapiens	Mutation(s): 0 Gene Names: PRPF31, PRP31
UniProt & NIH Common Fund Data Resources
Find proteins for Q8WWY3 (Homo sapiens) Explore Q8WWY3 Go to UniProtKB: Q8WWY3
PHAROS: Q8WWY3 GTEx: ENSG00000105618
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8WWY3
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 1
RNA comprising the 5' Stem-Loop RNA of U4snRNA	A [auth C], B [auth F]	33	N/A
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain I [auth E] SDF format, chain H [auth B] SDF format, chain G [auth A] MOL2 format, chain I [auth E] MOL2 format, chain H [auth B] MOL2 format, chain G [auth A] mmCIF format, chain I [auth E] mmCIF format, chain H [auth B] mmCIF format, chain G [auth A]	G [auth A], H [auth B], I [auth E]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth E] Interactions & Density Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.248 (Depositor), 0.232 (DCC)
R-Value Work: 0.206 (Depositor), 0.195 (DCC)
R-Value Observed: 0.208 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.555	α = 90
b = 99.896	β = 90
c = 169.645	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345	data collection
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2007-03-20

Deposition Author(s):

Liu, S.

Luehrmann, R.

Wahl, M.C.

Revision History (Full details and data files)

Version 1.0: 2007-03-20
Type: Initial release
Version 1.1: 2008-01-03
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.3: 2017-10-18
Changes: Refinement description
Version 1.4: 2018-01-24
Changes: Data collection
Version 1.5: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description