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- PDB-3s88: Crystal structure of Sudan Ebolavirus Glycoprotein (strain Gulu) ... -

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Basic information

Entry
Database: PDB / ID: 3s88
TitleCrystal structure of Sudan Ebolavirus Glycoprotein (strain Gulu) bound to 16F6
Components
  • (Envelope glycoprotein) x 2
  • 16F6 - Heavy chain
  • 16F6 - Light chain
KeywordsIMMUNE SYSTEM/VIRAL PROTEIN / Glycosylation / Viral membrane / IMMUNE SYSTEM-VIRAL PROTEIN complex
Function / homology
Function and homology information


clathrin-dependent endocytosis of virus by host cell / suppression by virus of host tetherin activity / membrane => GO:0016020 / entry receptor-mediated virion attachment to host cell / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane / extracellular region
Similarity search - Function
Filoviruses glycoprotein, extracellular domain / Filoviruses glycoprotein / Filovirus glycoprotein / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Envelope glycoprotein
Similarity search - Component
Biological speciesMus musculus (house mouse)
Sudan ebolavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.351 Å
AuthorsSaphire, E.O. / Dias, J.M. / Bale, S.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2011
Title: A shared structural solution for neutralizing ebolaviruses.
Authors: Dias, J.M. / Kuehne, A.I. / Abelson, D.M. / Bale, S. / Wong, A.C. / Halfmann, P. / Muhammad, M.A. / Fusco, M.L. / Zak, S.E. / Kang, E. / Kawaoka, Y. / Chandran, K. / Dye, J.M. / Saphire, E.O.
History
DepositionMay 27, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2011Group: 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_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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.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_seq_id / _struct_conn.ptnr2_label_asym_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 / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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
H: 16F6 - Heavy chain
I: Envelope glycoprotein
J: Envelope glycoprotein
L: 16F6 - Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,0636
Polymers99,2144
Non-polymers8492
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10750 Å2
ΔGint-50 kcal/mol
Surface area38790 Å2
MethodPISA
2
H: 16F6 - Heavy chain
I: Envelope glycoprotein
J: Envelope glycoprotein
L: 16F6 - Light chain
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)1,200,75472
Polymers1,190,56848
Non-polymers10,18624
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
crystal symmetry operation5_555z,x,y1
crystal symmetry operation6_566z,-x+1,-y+11
crystal symmetry operation7_665-z+1,-x+1,y1
crystal symmetry operation8_656-z+1,x,-y+11
crystal symmetry operation9_555y,z,x1
crystal symmetry operation10_656-y+1,z,-x+11
crystal symmetry operation11_566y,-z+1,-x+11
crystal symmetry operation12_665-y+1,-z+1,x1
Buried area182000 Å2
ΔGint-893 kcal/mol
Surface area412490 Å2
MethodPISA
3
H: 16F6 - Heavy chain
I: Envelope glycoprotein
J: Envelope glycoprotein
L: 16F6 - Light chain
hetero molecules

H: 16F6 - Heavy chain
I: Envelope glycoprotein
J: Envelope glycoprotein
L: 16F6 - Light chain
hetero molecules

H: 16F6 - Heavy chain
I: Envelope glycoprotein
J: Envelope glycoprotein
L: 16F6 - Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)300,18918
Polymers297,64212
Non-polymers2,5466
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area43770 Å2
ΔGint-213 kcal/mol
Surface area104850 Å2
MethodPISA
4
I: Envelope glycoprotein
J: Envelope glycoprotein
hetero molecules

I: Envelope glycoprotein
J: Envelope glycoprotein
hetero molecules

I: Envelope glycoprotein
J: Envelope glycoprotein
hetero molecules

H: 16F6 - Heavy chain
L: 16F6 - Light chain

H: 16F6 - Heavy chain
L: 16F6 - Light chain

H: 16F6 - Heavy chain
L: 16F6 - Light chain


Theoretical massNumber of molelcules
Total (without water)300,18918
Polymers297,64212
Non-polymers2,5466
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation16_455x-1/2,-y+1/2,-z+1/21
crystal symmetry operation20_545-z+1/2,x-1/2,-y+1/21
crystal symmetry operation24_554-y+1/2,-z+1/2,x-1/21
Buried area41140 Å2
ΔGint-202 kcal/mol
Surface area107490 Å2
MethodPISA
5
I: Envelope glycoprotein
hetero molecules

I: Envelope glycoprotein
hetero molecules

I: Envelope glycoprotein
hetero molecules

H: 16F6 - Heavy chain
J: Envelope glycoprotein
L: 16F6 - Light chain
hetero molecules

H: 16F6 - Heavy chain
J: Envelope glycoprotein
L: 16F6 - Light chain
hetero molecules

H: 16F6 - Heavy chain
J: Envelope glycoprotein
L: 16F6 - Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)300,18918
Polymers297,64212
Non-polymers2,5466
Water0
TypeNameSymmetry operationNumber
crystal symmetry operation14_555-x+1/2,-y+1/2,z+1/21
crystal symmetry operation18_555z+1/2,-x+1/2,-y+1/21
crystal symmetry operation22_555-y+1/2,z+1/2,-x+1/21
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area22820 Å2
ΔGint-104 kcal/mol
Surface area125800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)193.591, 193.591, 193.591
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: Antibody 16F6 - Heavy chain


Mass: 23600.488 Da / Num. of mol.: 1 / Fragment: UNP Residues 32-313
Source method: isolated from a genetically manipulated source
Details: Vaccination / Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#2: Protein Envelope glycoprotein / GP1 / GP


Mass: 33447.328 Da / Num. of mol.: 1 / Fragment: UNP Residues 473-639 / Mutation: I631V, Q638V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sudan ebolavirus / Strain: Gulu / Gene: GP / Plasmid: PDISPLAY / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q7T9D9
#3: Protein Envelope glycoprotein / GP2 / GP2


Mass: 18709.189 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sudan ebolavirus / Strain: Gulu / Gene: GP / Plasmid: PDISPLAY / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q7T9D9
#4: Antibody 16F6 - Light chain


Mass: 23457.027 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Vaccination / Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#5: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE

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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: 3.05 Å3/Da / Density % sol: 59.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.4
Details: 15% PEG 3350, 0.2 M Lithium citrate, pH 8.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 1, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.35→50 Å / Num. all: 17047 / Num. obs: 17047 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.3 % / Biso Wilson estimate: 68.6 Å2 / Rsym value: 0.088 / Net I/σ(I): 10.1
Reflection shellResolution: 3.35→3.43 Å / Redundancy: 5.9 % / Mean I/σ(I) obs: 1.7 / Num. unique all: 1881 / Rsym value: 0.825 / % 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: 3.351→45.63 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.908 / SU B: 70.373 / SU ML: 0.516 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R Free: 0.579 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27759 864 5.1 %RANDOM
Rwork0.22173 ---
all0.22462 15735 --
obs0.22173 16147 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 102.838 Å2
Refinement stepCycle: LAST / Resolution: 3.351→45.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5984 0 56 0 6040
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0226203
X-RAY DIFFRACTIONr_bond_other_d0.0010.024053
X-RAY DIFFRACTIONr_angle_refined_deg1.4261.9528464
X-RAY DIFFRACTIONr_angle_other_deg0.91439875
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3325781
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.74523.915258
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.59415920
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1811529
X-RAY DIFFRACTIONr_chiral_restr0.0770.2953
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216952
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021262
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_it1.5441.53914
X-RAY DIFFRACTIONr_mcbond_other0.1971.51585
X-RAY DIFFRACTIONr_mcangle_it2.89926283
X-RAY DIFFRACTIONr_scbond_it2.66932289
X-RAY DIFFRACTIONr_scangle_it4.724.52181
X-RAY DIFFRACTIONr_rigid_bond_restr1.495310256
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.351→3.437 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.406 73 -
Rwork0.297 1185 -
obs--100 %
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)
12.2053-0.56441.30980.1898-0.00961.37320.32820.0936-0.012-0.1664-0.2263-0.1324-0.2141-0.26-0.10190.38080.1644-0.00740.45180.08950.326283.20219.505275.2659
21.6-1.0897-0.48721.56461.14470.7096-0.4480.0701-0.41160.248-0.00050.460.30510.29570.44850.86050.49650.44920.41760.16320.332649.980512.7532.2057
30.5516-1.0254-0.6462.06720.55430.6867-0.0916-0.08060.1390.31350.09240.12290.34760.4866-0.00080.45540.43670.19060.72270.22030.242853.847833.193640.3219
42.3985-0.8740.61330.41930.22760.91980.26390.66140.1527-0.0523-0.2721-0.1533-0.07720.2380.00820.36210.14760.12150.47440.17930.300696.836616.598264.1143
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1H1 - 220
2X-RAY DIFFRACTION2I32 - 311
3X-RAY DIFFRACTION3J510 - 615
4X-RAY DIFFRACTION4L1 - 212

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