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- PDB-6hat: Globular domain of herpesvirus saimiri ORF57 -

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Basic information

Entry
Database: PDB / ID: 6hat
TitleGlobular domain of herpesvirus saimiri ORF57
ComponentsmRNA 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 / mRNA export factor ICP27 homolog
Similarity search - Component
Biological speciesSaimiriine herpesvirus 2 (Herpesvirus saimiri)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.856 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 / pdbx_seq_map_depositor_info
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.3Apr 10, 2019Group: Data collection / Source and taxonomy
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / entity_src_gen / pdbx_seq_map_depositor_info
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_variant / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.4Mar 30, 2022Group: Author supporting evidence / Database references / Derived calculations
Category: database_2 / pdbx_audit_support / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,3846
Polymers62,1352
Non-polymers2494
Water6,197344
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, SEC-MALLS confirmed homo-dimerisation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7830 Å2
ΔGint-60 kcal/mol
Surface area23110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.108, 118.652, 130.702
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: 31067.377 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: N-terminal Glycine non-native / 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: Chemical ChemComp-ZN / ZINC ION


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


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 344 / 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: 3.67 Å3/Da / Density % sol: 21.4 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.12 M Alcohols (0.2 M 1,6-Hexanediol; 0.2 M 1-Butanol; 0.2 M 1,2-Propanediol; 0.2M 2-Propanol; 0.2 M 1,4-Butanediol; 0.2M 1,3-Propanediol), 0.1 M (Imidazole, MES) Buffer System pH 6.5, 50 % ...Details: 0.12 M Alcohols (0.2 M 1,6-Hexanediol; 0.2 M 1-Butanol; 0.2 M 1,2-Propanediol; 0.2M 2-Propanol; 0.2 M 1,4-Butanediol; 0.2M 1,3-Propanediol), 0.1 M (Imidazole, MES) Buffer System pH 6.5, 50 % v/v GOL_P4K Mix (Morpheus HT96 D3 Molecular Dimensions)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.856→48.47 Å / Num. obs: 77002 / % possible obs: 99.83 % / Redundancy: 13.3 % / Biso Wilson estimate: 32.87 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.08329 / Rrim(I) all: 0.08668 / Net I/σ(I): 18.04
Reflection shellResolution: 1.856→1.923 Å / Redundancy: 13.5 % / Rmerge(I) obs: 0.9674 / Mean I/σ(I) obs: 2.55 / Num. unique obs: 7497 / CC1/2: 0.814 / Rrim(I) all: 1.005 / % possible all: 98.48

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.856→48.466 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.7
RfactorNum. reflection% reflectionSelection details
Rfree0.168 3810 2.59 %Random
Rwork0.1492 ---
obs0.1497 76996 99.79 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.856→48.466 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4293 0 10 344 4647
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0144483
X-RAY DIFFRACTIONf_angle_d1.1626107
X-RAY DIFFRACTIONf_dihedral_angle_d11.4642763
X-RAY DIFFRACTIONf_chiral_restr0.062726
X-RAY DIFFRACTIONf_plane_restr0.008764
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8565-1.880.25971380.27285143X-RAY DIFFRACTION96
1.88-1.90470.2741420.25235231X-RAY DIFFRACTION100
1.9047-1.93080.2441390.23025360X-RAY DIFFRACTION100
1.9308-1.95840.22431380.21215293X-RAY DIFFRACTION100
1.9584-1.98760.24891450.21065354X-RAY DIFFRACTION100
1.9876-2.01870.22271390.19845284X-RAY DIFFRACTION100
2.0187-2.05180.1941430.1865354X-RAY DIFFRACTION100
2.0518-2.08720.18191360.17815312X-RAY DIFFRACTION100
2.0872-2.12510.21451420.16745311X-RAY DIFFRACTION100
2.1251-2.1660.16911410.15335369X-RAY DIFFRACTION100
2.166-2.21020.16871450.14895276X-RAY DIFFRACTION100
2.2102-2.25830.15571440.14315296X-RAY DIFFRACTION100
2.2583-2.31080.17421390.13355356X-RAY DIFFRACTION100
2.3108-2.36860.16581410.13135316X-RAY DIFFRACTION100
2.3686-2.43260.16641420.13195345X-RAY DIFFRACTION100
2.4326-2.50420.16461400.13385297X-RAY DIFFRACTION100
2.5042-2.5850.14171440.13565315X-RAY DIFFRACTION100
2.585-2.67740.19011370.13895322X-RAY DIFFRACTION100
2.6774-2.78460.16441390.14215319X-RAY DIFFRACTION100
2.7846-2.91130.17681460.14795348X-RAY DIFFRACTION100
2.9113-3.06480.161420.15385332X-RAY DIFFRACTION100
3.0648-3.25670.17461420.15575315X-RAY DIFFRACTION100
3.2567-3.50810.17181440.15265299X-RAY DIFFRACTION100
3.5081-3.8610.13781400.13545338X-RAY DIFFRACTION100
3.861-4.41940.13921390.12345314X-RAY DIFFRACTION100
4.4194-5.56670.15661400.13015292X-RAY DIFFRACTION100
5.5667-48.4820.17181430.16725277X-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)
11.09780.6093-0.39053.3607-1.54861.971-0.105-0.0205-0.2-0.08170.1270.03060.3894-0.10320.03120.315-0.0190.03410.25760.0320.27762.33762.361882.1798
20.9185-0.26070.13321.1055-0.43531.1893-0.0574-0.1234-0.00980.12540.04760.0002-0.0488-0.03670.0180.1522-0.0136-0.00020.2044-0.00310.16211.86326.137281.9411
33.42732.13351.75554.19583.11814.43026.1401-18.703-3.54716.2698-5.5041-1.83235.78669.3078-0.64521.1378-0.057-0.15050.9749-0.00450.6732-7.604740.721992.2516
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 147 through 417)
2X-RAY DIFFRACTION2(chain 'B' and resid 145 through 417)
3X-RAY DIFFRACTION3(chain 'D' and resid 1 through 1)

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