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- PDB-5syb: Crystal structure of human PHF5A -

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Basic information

Entry
Database: PDB / ID: 5syb
TitleCrystal structure of human PHF5A
ComponentsPHD finger-like domain-containing protein 5A
KeywordsTRANSCRIPTION / Core component / SF3B complex / human spliceosome
Function / homology
Function and homology information


U12-type spliceosomal complex / U2-type spliceosomal complex / U2-type precatalytic spliceosome / U2-type prespliceosome assembly / U2 snRNP / precatalytic spliceosome / mRNA Splicing - Major Pathway / stem cell differentiation / spliceosomal complex / mRNA splicing, via spliceosome ...U12-type spliceosomal complex / U2-type spliceosomal complex / U2-type precatalytic spliceosome / U2-type prespliceosome assembly / U2 snRNP / precatalytic spliceosome / mRNA Splicing - Major Pathway / stem cell differentiation / spliceosomal complex / mRNA splicing, via spliceosome / nuclear matrix / nuclear speck / positive regulation of DNA-templated transcription / DNA binding / RNA binding / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
PHF5-like / PHF5-like protein
Similarity search - Domain/homology
PHD finger-like domain-containing protein 5A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.82 Å
AuthorsTsai, J.H.C. / Teng, T. / Zhu, P. / Fekkes, P. / Larsen, N.A.
CitationJournal: Nat Commun / Year: 2017
Title: Splicing modulators act at the branch point adenosine binding pocket defined by the PHF5A-SF3b complex.
Authors: Teng, T. / Tsai, J.H. / Puyang, X. / Seiler, M. / Peng, S. / Prajapati, S. / Aird, D. / Buonamici, S. / Caleb, B. / Chan, B. / Corson, L. / Feala, J. / Fekkes, P. / Gerard, B. / Karr, C. / ...Authors: Teng, T. / Tsai, J.H. / Puyang, X. / Seiler, M. / Peng, S. / Prajapati, S. / Aird, D. / Buonamici, S. / Caleb, B. / Chan, B. / Corson, L. / Feala, J. / Fekkes, P. / Gerard, B. / Karr, C. / Korpal, M. / Liu, X. / T Lowe, J. / Mizui, Y. / Palacino, J. / Park, E. / Smith, P.G. / Subramanian, V. / Wu, Z.J. / Zou, J. / Yu, L. / Chicas, A. / Warmuth, M. / Larsen, N. / Zhu, P.
History
DepositionAug 10, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2016Group: Structure summary
Revision 1.2Jun 7, 2017Group: Database references
Revision 1.3Mar 6, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PHD finger-like domain-containing protein 5A
B: PHD finger-like domain-containing protein 5A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,96812
Polymers25,3272
Non-polymers64110
Water1,74797
1
A: PHD finger-like domain-containing protein 5A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9846
Polymers12,6641
Non-polymers3205
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PHD finger-like domain-containing protein 5A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9846
Polymers12,6641
Non-polymers3205
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.116, 82.116, 82.116
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-349-

HOH

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Components

#1: Protein PHD finger-like domain-containing protein 5A / PHD finger-like domain protein 5A / Splicing factor 3B-associated 14 kDa protein / SF3b14b / P14b / ...PHD finger-like domain protein 5A / Splicing factor 3B-associated 14 kDa protein / SF3b14b / P14b / Rds3 homolog


Mass: 12663.710 Da / Num. of mol.: 2 / Mutation: C40S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PHF5A / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21* / References: UniProt: Q7RTV0
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H2O

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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: 1.83 Å3/Da / Density % sol: 32.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 100mM CHES pH9.5 0.8mM Sodium Citrate 0.5% beta-OG

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jun 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→58.1 Å / Num. obs: 318806 / % possible obs: 100 % / Redundancy: 10 % / Net I/σ(I): 15.2
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 8.1 % / Mean I/σ(I) obs: 2.7 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
xia2data reduction
xia2data scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.82→58.06 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.77 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.114
RfactorNum. reflection% reflectionSelection details
Rfree0.20289 876 5.2 %RANDOM
Rwork0.16798 ---
obs0.16979 16010 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 33.825 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.82→58.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1364 0 22 97 1483
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0191398
X-RAY DIFFRACTIONr_bond_other_d0.0020.021322
X-RAY DIFFRACTIONr_angle_refined_deg1.9811.9761872
X-RAY DIFFRACTIONr_angle_other_deg1.18333060
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4285178
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.71123.33360
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.37915242
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0221512
X-RAY DIFFRACTIONr_chiral_restr0.1230.2200
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211580
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02304
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.2532.973718
X-RAY DIFFRACTIONr_mcbond_other3.2492.969717
X-RAY DIFFRACTIONr_mcangle_it4.6564.42894
X-RAY DIFFRACTIONr_mcangle_other4.6564.428895
X-RAY DIFFRACTIONr_scbond_it5.1553.738680
X-RAY DIFFRACTIONr_scbond_other5.1523.738680
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.9485.373979
X-RAY DIFFRACTIONr_long_range_B_refined9.67225.5611643
X-RAY DIFFRACTIONr_long_range_B_other9.66925.5661644
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.818→1.865 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 76 -
Rwork0.245 1139 -
obs--99.92 %

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