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- PDB-4wzw: Crystal structure of human Puf-A in complex with DNA -

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Basic information

Entry
Database: PDB / ID: 4wzw
TitleCrystal structure of human Puf-A in complex with DNA
Components
  • DNA (5'-D(P*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*C)-3')
  • DNA (5'-D(P*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*G)-3')
  • Pumilio domain-containing protein KIAA0020
KeywordsDNA Binding Protein / RNA Binding Protein/DNA / Pumilio repeat protein / RNA Binding Protein-DNA complex
Function / homology
Function and homology information


regulation of protein ADP-ribosylation / regulation of translation / chromosome / mRNA binding / nucleolus / endoplasmic reticulum / DNA binding / RNA binding / nucleoplasm
Similarity search - Function
CPL domain / Pumilio homologue 3 / CPL (NUC119) domain / Pumilio homology domain / Pumilio homology domain (PUM-HD) profile. / Pumilio RNA-binding repeat profile. / Pumilio RNA-binding repeat / Pumilio-like repeats / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
DNA / DNA (> 10) / Pumilio homolog 3
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9516 Å
AuthorsQiu, C. / Hall, T.M.T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)Intramural Research Program United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: A divergent Pumilio repeat protein family for pre-rRNA processing and mRNA localization.
Authors: Qiu, C. / McCann, K.L. / Wine, R.N. / Baserga, S.J. / Hall, T.M.
History
DepositionNov 20, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 31, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 14, 2015Group: Database references
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_entity_src_syn / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pumilio domain-containing protein KIAA0020
B: DNA (5'-D(P*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*G)-3')
C: DNA (5'-D(P*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)68,1963
Polymers68,1963
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2580 Å2
ΔGint-23 kcal/mol
Surface area28740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.122, 69.122, 273.831
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322

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Components

#1: Protein Pumilio domain-containing protein KIAA0020 / HBV X-transactivated gene 5 protein / HBV XAg-transactivated protein 5 / Minor histocompatibility ...HBV X-transactivated gene 5 protein / HBV XAg-transactivated protein 5 / Minor histocompatibility antigen HA-8 / HLA-HA8 / Puf-A


Mass: 59049.676 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIAA0020, XTP5 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15397
#2: DNA chain DNA (5'-D(P*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*G)-3')


Mass: 4563.924 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*C)-3')


Mass: 4581.951 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
Compound detailsThe actual DNA sequence used for crystallization is: Mol.B: 5'-AAGGGCATGTCCGGGCATGTCCAA and Mol.C: ...The actual DNA sequence used for crystallization is: Mol.B: 5'-AAGGGCATGTCCGGGCATGTCCAA and Mol.C: 5'-TTGGACATGCCCGGACATGCCCTT. The protein-DNA interactions are sequence non-specific and mediated through the DNA phosphate backbone. The authors have modeled polyG for one strand and polyC for the other strand due to poor electron density of bases.

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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: 2.4 Å3/Da / Density % sol: 48.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 22.5% PEG3350, 0.2 M NH4OAc, 0.1 M bis-tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 2, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.95→50 Å / Num. obs: 14807 / % possible obs: 99.2 % / Redundancy: 13 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 29
Reflection shellResolution: 2.95→3 Å / % possible obs: 90.5 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.436 / Mean I/σ(I) obs: 3 / % possible all: 90.5

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WZR

4wzr


Resolution: 2.9516→48.116 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 28.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2651 1443 10.02 %
Rwork0.221 --
obs0.2255 14395 96.83 %
Solvent computationShrinkage radii: 1.1 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9516→48.116 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4029 612 0 0 4641
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024778
X-RAY DIFFRACTIONf_angle_d0.6416562
X-RAY DIFFRACTIONf_dihedral_angle_d15.9761868
X-RAY DIFFRACTIONf_chiral_restr0.041759
X-RAY DIFFRACTIONf_plane_restr0.003720
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9516-3.05710.40151260.32741107X-RAY DIFFRACTION85
3.0571-3.17950.33331320.30721204X-RAY DIFFRACTION93
3.1795-3.32420.36211390.25751264X-RAY DIFFRACTION97
3.3242-3.49940.33411440.2611284X-RAY DIFFRACTION98
3.4994-3.71850.27781420.23341290X-RAY DIFFRACTION99
3.7185-4.00550.30641460.21991300X-RAY DIFFRACTION99
4.0055-4.40840.23961490.21061329X-RAY DIFFRACTION99
4.4084-5.04570.23971480.19071330X-RAY DIFFRACTION99
5.0457-6.35470.27041530.23321382X-RAY DIFFRACTION100
6.3547-48.12250.21791640.19581462X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
18.7189-1.13771.57192.5674-0.91012.67040.22380.22070.3048-0.0668-0.33050.333-0.1157-0.57430.08490.38230.1416-0.06321.0454-0.00820.7055-26.265118.6553-15.1776
20.98680.48970.03330.794-1.13325.48990.02980.1624-0.0966-0.17-0.2954-0.23110.15080.78770.20630.3540.2641-0.00740.97710.05290.62079.290319.7955-34.3571
35.5704-0.59221.72025.6037-2.4048.2262-0.6181-0.44490.35031.1251-0.3006-0.9927-1.90251.33111.03581.2035-0.4649-0.29511.44490.24070.732117.92348.3437-59.1542
46.39211.136-1.84223.2721-1.26714.2701-0.35110.72221.9549-0.49980.49440.989-1.4266-0.2791-0.16891.3412-0.00890.10841.32820.232.9361-2.204737.7846-30.546
55.82232.26460.54271.5726-0.11291.6599-0.86260.272-0.703-0.1584-0.16460.35880.11720.33950.85621.61190.0920.25261.319-0.21341.7794-0.900235.8957-31.4412
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 129 through 276 )
2X-RAY DIFFRACTION2chain 'A' and (resid 277 through 553 )
3X-RAY DIFFRACTION3chain 'A' and (resid 554 through 645 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 14 )
5X-RAY DIFFRACTION5chain 'C' and (resid 1 through 16 )

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