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- PDB-8gxm: HUMAN SUGP1 433-586 -

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Basic information

Entry
Database: PDB / ID: 8gxm
TitleHUMAN SUGP1 433-586
ComponentsSURP and G-patch domain-containing protein 1
KeywordsRNA BINDING PROTEIN / pre-mRNA splicing.
Function / homology
Function and homology information


mRNA Splicing - Major Pathway / RNA splicing / spliceosomal complex / mRNA processing / RNA binding / nucleoplasm
Similarity search - Function
SURP and G-patch domain-containing protein 1/2 / G-patch domain / G-patch domain profile. / G-patch domain / glycine rich nucleic binding domain / SWAP/Surp / SWAP/Surp superfamily / Surp module / SURP motif repeat profile. / Suppressor-of-White-APricot splicing regulator
Similarity search - Domain/homology
SURP and G-patch domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 Å
AuthorsXu, K. / Tong, L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM118093 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: DHX15 is involved in SUGP1-mediated RNA missplicing by mutant SF3B1 in cancer.
Authors: Zhang, J. / Huang, J. / Xu, K. / Xing, P. / Huang, Y. / Liu, Z. / Tong, L. / Manley, J.L.
History
DepositionSep 20, 2022Deposition site: PDBJ / Processing site: RCSB
Revision 1.0Dec 14, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SURP and G-patch domain-containing protein 1
B: SURP and G-patch domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)36,7692
Polymers36,7692
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2050 Å2
ΔGint-16 kcal/mol
Surface area15540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.160, 60.160, 177.768
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z+1/2

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Components

#1: Protein SURP and G-patch domain-containing protein 1 / RNA-binding protein RBP / Splicing factor 4


Mass: 18384.746 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SUGP1, SF4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8IWZ8

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.3 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Bis-Tris (pH 7.5), 25% (w/v) polyethylene glycol 3350.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 8896 / % possible obs: 99.8 % / Redundancy: 7.8 % / CC1/2: 0.999 / Net I/σ(I): 27.5
Reflection shellResolution: 2.8→2.91 Å / Num. unique obs: 887 / CC1/2: 0.87

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Processing

Software
NameVersionClassification
XDSdata scaling
Cootmodel building
PHENIX1.17.1_3660phasing
PHENIX1.17.1_3660refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8GXL

8gxl


Resolution: 2.81→44.95 Å / SU ML: 0.3656 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 32.9018
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2971 884 9.94 %
Rwork0.2173 8010 -
obs0.2252 8894 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 84.9 Å2
Refinement stepCycle: LAST / Resolution: 2.81→44.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2058 0 0 0 2058
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00962095
X-RAY DIFFRACTIONf_angle_d1.12952787
X-RAY DIFFRACTIONf_chiral_restr0.049275
X-RAY DIFFRACTIONf_plane_restr0.0058356
X-RAY DIFFRACTIONf_dihedral_angle_d6.5726253
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.81-2.980.35881480.28011338X-RAY DIFFRACTION99.27
2.98-3.210.35031430.28241315X-RAY DIFFRACTION100
3.21-3.530.3321420.24591353X-RAY DIFFRACTION100
3.54-4.050.28141440.2321333X-RAY DIFFRACTION99.93
4.05-5.090.28281440.19941334X-RAY DIFFRACTION100
5.1-44.950.28881630.19631337X-RAY DIFFRACTION99.93

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