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- PDB-6hau: KSHV PAN RNA Mta-response element fragment complexed with the glo... -

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Basic information

Entry
Database: PDB / ID: 6hau
TitleKSHV PAN RNA Mta-response element fragment complexed with the globular domain of herpesvirus saimiri ORF57
Components
  • MRE fragment of PAN RNA
  • mRNA export factor ICP27 homolog
KeywordsRNA BINDING PROTEIN / Homodimer / ICP27 / IHD / RNA
Function / homology
Function and homology information


host cell cytoplasm / molecular adaptor activity / host cell nucleus / regulation of DNA-templated transcription / RNA binding / metal ion binding
Similarity search - Function
Herpesvirus ICP27-like / Herpesvirus transcriptional regulator family
Similarity search - Domain/homology
ACETATE ION / RNA / RNA (> 10) / mRNA export factor ICP27 homolog
Similarity search - Component
Biological speciesSaimiriine herpesvirus 2 (Herpesvirus saimiri)
Human herpesvirus 8
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsTunnicliffe, R.B. / Levy, C. / Ruiz Nivia, H.D. / Sandri-Goldin, R.M. / Golovanov, A.P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI107803 United States
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: Structural identification of conserved RNA binding sites in herpesvirus ORF57 homologs: implications for PAN RNA recognition.
Authors: Tunnicliffe, R.B. / Levy, C. / Ruiz Nivia, H.D. / Sandri-Goldin, R.M. / Golovanov, A.P.
History
DepositionAug 8, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 21, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 13, 2019Group: Data collection / Database references
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Apr 10, 2019Group: Data collection / Source and taxonomy
Category: database_PDB_rev / database_PDB_rev_record / entity_src_gen
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_variant
Revision 1.4Mar 30, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.5May 1, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: mRNA export factor ICP27 homolog
B: mRNA export factor ICP27 homolog
D: MRE fragment of PAN RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,0506
Polymers66,8603
Non-polymers1903
Water7,764431
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, SEC-MALLS of Apo protein indicated homo-dimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8880 Å2
ΔGint-59 kcal/mol
Surface area24240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.657, 105.261, 118.554
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein mRNA export factor ICP27 homolog / 52 kDa immediate-early phosphoprotein / EB2 protein homolog


Mass: 30739.115 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saimiriine herpesvirus 2 (strain 11) / Strain: 11 / Gene: EJRF1, ORF57 / Plasmid: pET-21a / Production host: Escherichia coli (E. coli) / Variant (production host): T7 express / References: UniProt: P13199
#2: RNA chain MRE fragment of PAN RNA


Mass: 5382.189 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: PAN RNA Mta-responsive element fragment, bases 34-50
Source: (synth.) Human herpesvirus 8
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 431 / 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: 2.53 Å3/Da / Density % sol: 51.44 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.06 M divalents (0.3M Magnesium chloride hexahydrate; 0.3M Calcium chloride dehydrate), 0.1 M (Imidazole, MES) Buffer System pH 6.5, 50 % v/v GOL_P4K (Morpheus HT96 A3 Molecular Dimensions)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9282 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9282 Å / Relative weight: 1
ReflectionResolution: 1.858→78.71 Å / Num. obs: 62577 / % possible obs: 99.89 % / Redundancy: 7.5 % / Biso Wilson estimate: 28.14 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.07311 / Rrim(I) all: 0.07854 / Net I/σ(I): 18.23
Reflection shellResolution: 1.858→1.925 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.7248 / Mean I/σ(I) obs: 2.67 / Num. unique obs: 6135 / CC1/2: 0.798 / Rrim(I) all: 0.7766 / % possible all: 99.79

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Apo HVS ORF57

Resolution: 1.86→78.71 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.81
RfactorNum. reflection% reflectionSelection details
Rfree0.197 5953 5 %Random
Rwork0.158 ---
obs0.16 62543 99.7 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.86→78.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4304 119 6 431 4860
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084692
X-RAY DIFFRACTIONf_angle_d0.9246428
X-RAY DIFFRACTIONf_dihedral_angle_d10.0412879
X-RAY DIFFRACTIONf_chiral_restr0.047765
X-RAY DIFFRACTIONf_plane_restr0.006795
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8582-1.87930.27332230.27053817X-RAY DIFFRACTION100
1.8793-1.90140.27422100.2563692X-RAY DIFFRACTION99
1.9014-1.92460.24972100.23253716X-RAY DIFFRACTION100
1.9246-1.9490.25031850.22783859X-RAY DIFFRACTION100
1.949-1.97460.23092070.21193735X-RAY DIFFRACTION99
1.9746-2.00170.22791950.19913731X-RAY DIFFRACTION100
2.0017-2.03030.21761850.19153814X-RAY DIFFRACTION100
2.0303-2.06060.21632360.19153751X-RAY DIFFRACTION100
2.0606-2.09280.1921960.19473773X-RAY DIFFRACTION100
2.0928-2.12710.21452090.19163720X-RAY DIFFRACTION100
2.1271-2.16380.22391820.18243833X-RAY DIFFRACTION100
2.1638-2.20310.1881860.1613723X-RAY DIFFRACTION100
2.2031-2.24550.16832140.15453772X-RAY DIFFRACTION100
2.2455-2.29130.19871700.15093804X-RAY DIFFRACTION100
2.2913-2.34120.20752180.14693766X-RAY DIFFRACTION100
2.3412-2.39560.19321780.14553767X-RAY DIFFRACTION100
2.3956-2.45560.18571910.15033815X-RAY DIFFRACTION100
2.4556-2.52190.19431930.14933761X-RAY DIFFRACTION100
2.5219-2.59620.23821670.14993801X-RAY DIFFRACTION100
2.5962-2.680.18082170.15163769X-RAY DIFFRACTION100
2.68-2.77580.20561650.16143818X-RAY DIFFRACTION100
2.7758-2.88690.21751810.15243735X-RAY DIFFRACTION100
2.8869-3.01830.1862040.15673802X-RAY DIFFRACTION100
3.0183-3.17740.20921820.15823778X-RAY DIFFRACTION100
3.1774-3.37650.19432370.16113730X-RAY DIFFRACTION100
3.3765-3.63720.21881960.15293777X-RAY DIFFRACTION100
3.6372-4.00320.17071970.14213775X-RAY DIFFRACTION100
4.0032-4.58240.17721790.12243796X-RAY DIFFRACTION100
4.5824-5.77310.16491920.12833774X-RAY DIFFRACTION100
5.7731-78.78340.18532480.17293709X-RAY DIFFRACTION100
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)
10.7313-0.11160.04261.92040.7561.4603-0.0696-0.10660.09320.308-0.06430.1576-0.143-0.12120.08590.24690.0179-0.00110.2104-0.03660.2162-2.8393-2.179220.8443
20.98270.03960.05271.20930.21120.6064-0.06630.0720.1186-0.08050.04630.0038-0.10170.01630.0130.1568-0.00280.00120.1903-0.00730.1442-3.908-9.352-1.716
33.6536-2.24220.79344.79793.26924.30140.43560.59951.3612-0.60370.12560.0353-2.1305-0.2085-0.30560.94190.04070.16160.47710.20171.27849.159513.91863.3161
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN 'A' AND RESID 145 THROUGH 417)
2X-RAY DIFFRACTION2(CHAIN 'B' AND RESID 145 THROUGH 417)
3X-RAY DIFFRACTION3(CHAIN 'D' AND RESID 34 THROUGH 47)

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