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- PDB-6e5x: Crystal structure of Ebola virus VP30 C-terminus/RBBP6 peptide complex -

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Basic information

Entry
Database: PDB / ID: 6e5x
TitleCrystal structure of Ebola virus VP30 C-terminus/RBBP6 peptide complex
Components
  • E3 ubiquitin-protein ligase RBBP6
  • Minor nucleoprotein VP30
KeywordsVIRAL PROTEIN
Function / homology
Function and homology information


somite development / RHOBTB1 GTPase cycle / regulation of DNA replication / embryonic organ development / RING-type E3 ubiquitin transferase / multicellular organism growth / mRNA processing / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation ...somite development / RHOBTB1 GTPase cycle / regulation of DNA replication / embryonic organ development / RING-type E3 ubiquitin transferase / multicellular organism growth / mRNA processing / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / chromosome / viral nucleocapsid / ubiquitin-dependent protein catabolic process / in utero embryonic development / host cell cytoplasm / DNA replication / nuclear speck / protein ubiquitination / symbiont-mediated suppression of host innate immune response / centrosome / DNA damage response / protein kinase binding / nucleolus / protein-containing complex / RNA binding / zinc ion binding / identical protein binding / nucleus / cytosol
Similarity search - Function
Zinc knuckle CX2CX3GHX4C / E3 ubiquitin-protein ligase RBBP6 family / Zinc knuckle / Four Helix Bundle (Hemerythrin (Met), subunit A) - #1160 / DWNN domain / DWNN domain / DWNN domain profile. / DWNN / Transcriptional activator VP30, Filoviridae type / Ebola virus-specific transcription factor VP30 ...Zinc knuckle CX2CX3GHX4C / E3 ubiquitin-protein ligase RBBP6 family / Zinc knuckle / Four Helix Bundle (Hemerythrin (Met), subunit A) - #1160 / DWNN domain / DWNN domain / DWNN domain profile. / DWNN / Transcriptional activator VP30, Filoviridae type / Ebola virus-specific transcription factor VP30 / U-box domain / U-box domain / Ring finger / Four Helix Bundle (Hemerythrin (Met), subunit A) / Zinc finger RING-type profile. / Zinc finger, RING-type / zinc finger / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Zinc finger, RING/FYVE/PHD-type / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Transcriptional activator VP30 / E3 ubiquitin-protein ligase RBBP6
Similarity search - Component
Biological speciesZaire ebolavirus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsLiu, D. / Small, G.I. / Leung, D.W. / Amarasinghe, G.K.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI120943 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)AI123926 United States
CitationJournal: Cell / Year: 2018
Title: Protein Interaction Mapping Identifies RBBP6 as a Negative Regulator of Ebola Virus Replication.
Authors: Batra, J. / Hultquist, J.F. / Liu, D. / Shtanko, O. / Von Dollen, J. / Satkamp, L. / Jang, G.M. / Luthra, P. / Schwarz, T.M. / Small, G.I. / Arnett, E. / Anantpadma, M. / Reyes, A. / Leung, ...Authors: Batra, J. / Hultquist, J.F. / Liu, D. / Shtanko, O. / Von Dollen, J. / Satkamp, L. / Jang, G.M. / Luthra, P. / Schwarz, T.M. / Small, G.I. / Arnett, E. / Anantpadma, M. / Reyes, A. / Leung, D.W. / Kaake, R. / Haas, P. / Schmidt, C.B. / Schlesinger, L.S. / LaCount, D.J. / Davey, R.A. / Amarasinghe, G.K. / Basler, C.F. / Krogan, N.J.
History
DepositionJul 23, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Minor nucleoprotein VP30
B: E3 ubiquitin-protein ligase RBBP6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0613
Polymers16,0212
Non-polymers401
Water2,684149
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1200 Å2
ΔGint-18 kcal/mol
Surface area8700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.600, 45.600, 158.710
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Minor nucleoprotein VP30 / Transcription activator VP30


Mass: 14407.747 Da / Num. of mol.: 1 / Fragment: C-terminal domain (UNP residues 140-266)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zaire ebolavirus (strain Kikwit-95) / Strain: Kikwit-95 / Gene: VP30 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q77DJ5
#2: Protein/peptide E3 ubiquitin-protein ligase RBBP6 / Proliferation potential-related protein / Protein P2P-R / RING-type E3 ubiquitin transferase RBBP6 ...Proliferation potential-related protein / Protein P2P-R / RING-type E3 ubiquitin transferase RBBP6 / Retinoblastoma-binding Q protein 1 / RBQ-1 / Retinoblastoma-binding protein 6 / p53-associated cellular protein of testis


Mass: 1612.946 Da / Num. of mol.: 1 / Fragment: UNP residues 554-568 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q7Z6E9
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 2.57 Å3/Da / Density % sol: 52.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M calcium acetate hydrate, 0.1 M sodium cacodylate trihydrate, pH 6.5, 18% w/v PEG8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.00003 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Aug 25, 2017
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 1.5→43.83 Å / Num. obs: 27964 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 16.7 % / Biso Wilson estimate: 26.75 Å2 / CC1/2: 0.3 / Rmerge(I) obs: 0.05 / Rrim(I) all: 0.05 / Net I/σ(I): 30.4
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 10.5 % / Rmerge(I) obs: 0.02 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 1327 / CC1/2: 0.3 / Rrim(I) all: 0.02 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5VAP

5vap


Resolution: 1.5→43.83 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.729 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.07 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23021 1317 4.7 %RANDOM
Rwork0.18913 ---
obs0.19109 26511 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.79 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.5→43.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1105 0 1 149 1255
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0141131
X-RAY DIFFRACTIONr_bond_other_d00.0171070
X-RAY DIFFRACTIONr_angle_refined_deg0.6591.6541541
X-RAY DIFFRACTIONr_angle_other_deg0.8451.6182508
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9325138
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.86721.34652
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.90715195
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.034158
X-RAY DIFFRACTIONr_chiral_restr0.0380.2152
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.021224
X-RAY DIFFRACTIONr_gen_planes_other00.02192
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_it3.5513.011558
X-RAY DIFFRACTIONr_mcbond_other3.5252.999557
X-RAY DIFFRACTIONr_mcangle_it5.1914.476694
X-RAY DIFFRACTIONr_mcangle_other5.1964.492695
X-RAY DIFFRACTIONr_scbond_it4.9743.403573
X-RAY DIFFRACTIONr_scbond_other4.9713.416574
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.5074.954848
X-RAY DIFFRACTIONr_long_range_B_refined8.69956.0244705
X-RAY DIFFRACTIONr_long_range_B_other8.63355.6334591
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.39 82 -
Rwork0.342 1869 -
obs--97.84 %

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