4NHO | pdb_00004nho

Structure of the spliceosomal DEAD-box protein Prp28


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.218 (Depositor), 0.221 (DCC) 
  • R-Value Work: 
    0.193 (Depositor), 0.196 (DCC) 
  • R-Value Observed: 
    0.194 (Depositor) 

Starting Model: experimental
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This is version 1.5 of the entry. See complete history

Literature

Structural and functional analysis of the human spliceosomal DEAD-box helicase Prp28.

Mohlmann, S.Mathew, R.Neumann, P.Schmitt, A.Luhrmann, R.Ficner, R.

(2014) Acta Crystallogr D Biol Crystallogr 70: 1622-1630

  • DOI: https://doi.org/10.1107/S1399004714006439
  • Primary Citation Related Structures: 
    4NHO

  • PubMed Abstract: 

    The DEAD-box protein Prp28 is essential for pre-mRNA splicing as it plays a key role in the formation of an active spliceosome. Prp28 participates in the release of the U1 snRNP from the 5'-splice site during association of the U5·U4/U6 tri-snRNP, which is a crucial step in the transition from a pre-catalytic spliceosome to an activated spliceosome. Here, it is demonstrated that the purified helicase domain of human Prp28 (hPrp28ΔN) binds ADP, whereas binding of ATP and ATPase activity could not be detected. ATP binding could not be observed for purified full-length hPrp28 either, but within an assembled spliceosomal complex hPrp28 gains ATP-binding activity. In order to understand the structural basis for the ATP-binding deficiency of isolated hPrp28, the crystal structure of hPrp28ΔN was determined at 2.0 Å resolution. In the crystal the helicase domain adopts a wide-open conformation, as the two RecA-like domains are extraordinarily displaced from the productive ATPase conformation. Binding of ATP is hindered by a closed conformation of the P-loop, which occupies the space required for the γ-phosphate of ATP.


  • Organizational Affiliation
    • Molecular Structural Biology, Georg-August-University Göttingen, Justus-von-Liebig Weg 11, 37077 Göttingen, Germany.

Macromolecule Content 

  • Total Structure Weight: 56.1 kDa 
  • Atom Count: 3,833 
  • Modeled Residue Count: 443 
  • Deposited Residue Count: 488 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Probable ATP-dependent RNA helicase DDX23488Homo sapiensMutation(s): 0 
Gene Names: DDX23
EC: 3.6.4.13
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BUQ8 (Homo sapiens)
Explore Q9BUQ8 
Go to UniProtKB:  Q9BUQ8
PHAROS:  Q9BUQ8
GTEx:  ENSG00000174243 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BUQ8
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CXS

Query on CXS



Download:Ideal Coordinates CCD File
I [auth A]3-CYCLOHEXYL-1-PROPYLSULFONIC ACID
C9 H19 N O3 S
PJWWRFATQTVXHA-UHFFFAOYSA-N
HG

Query on HG



Download:Ideal Coordinates CCD File
J [auth A]MERCURY (II) ION
Hg
BQPIGGFYSBELGY-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
B [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
G [auth A],
H [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CSO
Query on CSO
A
L-PEPTIDE LINKINGC3 H7 N O3 SCYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.218 (Depositor), 0.221 (DCC) 
  • R-Value Work:  0.193 (Depositor), 0.196 (DCC) 
  • R-Value Observed: 0.194 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 125.43α = 90
b = 136.77β = 90
c = 73.22γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
SOLOMONphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
MAR345dtbdata collection
MOSFLMdata reduction
SHARPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-06-18
    Type: Initial release
  • Version 1.1: 2014-09-24
    Changes: Database references
  • Version 1.2: 2019-09-04
    Changes: Data collection, Derived calculations
  • Version 1.3: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2023-12-06
    Changes: Data collection
  • Version 1.5: 2024-11-27
    Changes: Structure summary