4FXX | pdb_00004fxx

Structure of SF1 coiled-coil domain

PDB DOI: https://doi.org/10.2210/pdb4FXX/pdb

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

Deposited: 2012-07-03 Released: 2013-01-16
Deposition Author(s): Gupta, A., Bauer, W.J., Wang, W., Kielkopf, C.L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.48 Å
R-Value Free:
0.270 (Depositor), 0.269 (DCC)
R-Value Work:
0.236 (Depositor), 0.232 (DCC)
R-Value Observed:
0.239 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Structure of Phosphorylated SF1 Bound to U2AF(65) in an Essential Splicing Factor Complex.

Wang, W., Maucuer, A., Gupta, A., Manceau, V., Thickman, K.R., Bauer, W.J., Kennedy, S.D., Wedekind, J.E., Green, M.R., Kielkopf, C.L.

(2013) Structure 21: 197-208

PubMed: 23273425 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1016/j.str.2012.10.020
Primary Citation Related Structures:
4FXW, 4FXX

PubMed Abstract:
The essential splicing factors U2AF⁶⁵ and SF1 cooperatively bind consensus sequences at the 3' end of introns. Phosphorylation of SF1 on a highly conserved "SPSP" motif enhances its interaction with U2AF⁶⁵ and the pre-mRNA. Here, we reveal that phosphorylation induces essential conformational changes in SF1 and in the SF1/U2AF⁶⁵/3' splice site complex. Crystal structures of the phosphorylated (P)SF1 domain bound to the C-terminal domain of U2AF⁶⁵ at 2.29 Å resolution and of the unphosphorylated SF1 domain at 2.48 Å resolution demonstrate that phosphorylation induces a disorder-to-order transition within a previously unknown SF1/U2AF⁶⁵ interface. We find by small-angle X-ray scattering that the local folding of the SPSP motif transduces into global conformational changes in the nearly full-length (P)SF1/U2AF⁶⁵/3' splice site assembly. We further determine that SPSP phosphorylation and the SF1/U2AF⁶⁵ interface are essential in vivo. These results offer a structural prototype for phosphorylation-dependent control of pre-mRNA splicing factors.

Organizational Affiliation

Center for RNA Biology and Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA.

Macromolecule Content

Total Structure Weight: 51.81 kDa
Atom Count: 2,990
Modeled Residue Count: 365
Deposited Residue Count: 448
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Splicing factor 1	A, B, C, D	112	Homo sapiens	Mutation(s): 0 Gene Names: SF1, ZFM1, ZNF162
UniProt & NIH Common Fund Data Resources
Find proteins for Q15637 (Homo sapiens) Explore Q15637 Go to UniProtKB: Q15637
PHAROS: Q15637 GTEx: ENSG00000168066
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q15637
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MLI Query on MLI Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain K [auth C] MOL2 format, chain F [auth A] MOL2 format, chain K [auth C] mmCIF format, chain F [auth A] mmCIF format, chain K [auth C]	F [auth A], K [auth C]	MALONATE ION C₃ H₂ O₄ OFOBLEOULBTSOW-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain K [auth C] Interactions & Density Focus chain F [auth A] Focus chain K [auth C]
IMD Query on IMD Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain I [auth C] SDF format, chain J [auth C] SDF format, chain L [auth D] SDF format, chain N [auth D] SDF format, chain M [auth D] SDF format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain I [auth C] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] MOL2 format, chain N [auth D] MOL2 format, chain M [auth D] MOL2 format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B] mmCIF format, chain I [auth C] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D] mmCIF format, chain N [auth D] mmCIF format, chain M [auth D] mmCIF format, chain E [auth A]	E [auth A] G [auth B] H [auth B] I [auth C] J [auth C] E [auth A], G [auth B], H [auth B], I [auth C], J [auth C], L [auth D], M [auth D], N [auth D]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth C] Focus chain J [auth C] Focus chain L [auth D] Focus chain M [auth D] Focus chain N [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth C] Focus chain J [auth C] Focus chain L [auth D] Focus chain M [auth D] Focus chain N [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.48 Å
R-Value Free: 0.270 (Depositor), 0.269 (DCC)
R-Value Work: 0.236 (Depositor), 0.232 (DCC)
R-Value Observed: 0.239 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.03	α = 90
b = 37.97	β = 107.38
c = 144.68	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
Web-Ice	data collection
MOSFLM	data reduction
PHENIX	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2013-01-16

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-01-16
Type: Initial release
Version 1.1: 2013-02-27
Changes: Database references
Version 1.2: 2024-02-28
Changes: Data collection, Database references, Derived calculations, Refinement description