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- PDB-3ve0: Crystal structure of Sudan Ebolavirus Glycoprotein (strain Bonifa... -

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Basic information

Entry
Database: PDB / ID: 3ve0
TitleCrystal structure of Sudan Ebolavirus Glycoprotein (strain Boniface) bound to 16F6
Components
  • (Envelope glycoprotein) x 2
  • 16F6 Antibody chain A
  • 16F6 Antibody chain B
KeywordsImmune system/viral protein / Ebola / Sudan / Glycoprotein / Virus surface / Immune system-viral protein complex
Function / homology
Function and homology information


clathrin-dependent endocytosis of virus by host cell / symbiont-mediated-mediated suppression of host tetherin activity / entry receptor-mediated virion attachment to host cell / symbiont-mediated suppression of host innate immune response / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane / extracellular region / membrane
Similarity search - Function
: / Filoviruses glycoprotein, extracellular domain / Filoviruses glycoprotein / Filovirus glycoprotein / Envelope glycoprotein GP2-like, HR1-HR2 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Envelope glycoprotein
Similarity search - Component
Biological speciesSudan ebolavirus
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.353 Å
AuthorsSaphire, E.O. / Bale, S. / Dias, J.M.
CitationJournal: Viruses / Year: 2012
Title: Structural basis for differential neutralization of ebolaviruses.
Authors: Bale, S. / Dias, J.M. / Fusco, M.L. / Hashiguchi, T. / Wong, A.C. / Liu, T. / Keuhne, A.I. / Li, S. / Woods, V.L. / Chandran, K. / Dye, J.M. / Saphire, E.O.
History
DepositionJan 6, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2012Group: Database references
Revision 1.2May 30, 2012Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _citation.country ..._chem_comp.pdbx_synonyms / _citation.country / _citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
I: Envelope glycoprotein
J: Envelope glycoprotein
A: 16F6 Antibody chain A
B: 16F6 Antibody chain B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,4706
Polymers99,2974
Non-polymers1,1732
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10790 Å2
ΔGint-51 kcal/mol
Surface area38900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)194.859, 194.859, 194.859
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

#1: Protein Envelope glycoprotein / GP1


Mass: 33404.312 Da / Num. of mol.: 1 / Fragment: Sudan Boniface Glycoprotein
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sudan ebolavirus / Strain: Boniface-76 / Gene: GP / Plasmid: pDISPLAY / Cell line (production host): HEK-293T / Production host: homo sapiens (human) / References: UniProt: Q66814
#2: Protein Envelope glycoprotein / GP2


Mass: 18749.258 Da / Num. of mol.: 1 / Fragment: 16F6 chain A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sudan ebolavirus / Strain: Boniface-76 / Gene: GP / Plasmid: pDISPLAY / Cell line (production host): HEK-293T / Production host: homo sapiens (human) / References: UniProt: Q66814
#3: Antibody 16F6 Antibody chain A


Mass: 23686.604 Da / Num. of mol.: 1 / Fragment: 16F6 chain B / Source method: isolated from a natural source
Details: Antibody raised by injecting mice with irradiated virus
Source: (natural) Mus musculus (house mouse)
#4: Antibody 16F6 Antibody chain B


Mass: 23457.027 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Antibody raised by injecting mice with irradiated virus
Source: (natural) Mus musculus (house mouse)
#5: Polysaccharide alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
Has protein modificationY

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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: 3.1 Å3/Da / Density % sol: 60.38 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 8.4
Details: 15% (w/v) PEG 3350, 0.2 M lithium citrate, and 1.5% benzamidine hydrochloride, pH 8.4, VAPOR DIFFUSION, HANGING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1159 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 1, 2008
RadiationMonochromator: Double flat crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1159 Å / Relative weight: 1
ReflectionResolution: 3.35→50 Å / Num. all: 17818 / Num. obs: 17818 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 8.4 % / Rmerge(I) obs: 0.049 / Rsym value: 0.079 / Net I/σ(I): 13.4
Reflection shellResolution: 3.35→3.47 Å / Redundancy: 8.5 % / Rmerge(I) obs: 0.691 / Mean I/σ(I) obs: 2.8 / Rsym value: 0.777 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3CSY

3csy


Resolution: 3.353→45.93 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.905 / SU B: 71.763 / SU ML: 0.524 / Cross valid method: THROUGHOUT / ESU R Free: 0.59 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28949 908 5.1 %RANDOM
Rwork0.22173 ---
obs0.22523 16866 99.79 %-
all-17818 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 142.918 Å2
Refinement stepCycle: LAST / Resolution: 3.353→45.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5924 0 78 0 6002
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0226163
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5381.9618409
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0495776
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.56423.944251
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.8315906
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2881528
X-RAY DIFFRACTIONr_chiral_restr0.1030.2955
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214683
X-RAY DIFFRACTIONr_gen_planes_other
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_it2.4281.53889
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.39326239
X-RAY DIFFRACTIONr_scbond_it3.16432274
X-RAY DIFFRACTIONr_scangle_it5.4054.52170
X-RAY DIFFRACTIONr_rigid_bond_restr2.28836163
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.353→3.439 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.459 85 -
Rwork0.296 1212 -
obs--99.85 %
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)
10.34510.50530.14070.2479-0.3418-0.7253-0.03840.07830.0465-0.20440.05470.0549-0.2286-0.0599-0.01640.003-0.0586-0.02990.0325-0.04840.025450.720713.327332.8604
2-0.68790.46380.2084-0.22990.1786-0.85170.00150.0196-0.1049-0.0252-0.02410.06360.091-0.09220.02250.12140.06070.0230.12560.0260.059454.438933.00440.8225
30.38970.01090.1552-0.05930.02570.0864-0.00650.0011-0.0099-0.0007-0.0137-0.0038-0.0069-0.00440.02020.09010.0022-0.00420.082-0.00460.091684.105319.724875.9518
40.3556-0.14960.19370.0858-0.04160.18160.01830.03930.0270.0051-0.03-0.02330.00840.02420.01170.0741-0.00050.00420.07590.00010.083797.349916.661864.5217
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1I32 - 311
2X-RAY DIFFRACTION2J510 - 614
3X-RAY DIFFRACTION3A1 - 220
4X-RAY DIFFRACTION4B1 - 212

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