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- PDB-6vkm: Crystal Structure of Stabilized GP from Makona Variant of Ebola Virus -

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Basic information

Entry
Database: PDB / ID: 6vkm
TitleCrystal Structure of Stabilized GP from Makona Variant of Ebola Virus
ComponentsVirion spike glycoprotein
KeywordsVIRAL PROTEIN / virus / glycoprotein / fusion / trimer / prefusion / EBOV
Function / homology
Function and homology information


host cell endoplasmic reticulum / viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / suppression by virus of host tetherin activity / host cell cytoplasm / entry receptor-mediated virion attachment to host cell / membrane => GO:0016020 / symbiont entry into host cell / membrane raft / fusion of virus membrane with host endosome membrane ...host cell endoplasmic reticulum / viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / suppression by virus of host tetherin activity / host cell cytoplasm / entry receptor-mediated virion attachment to host cell / membrane => GO:0016020 / symbiont entry into host cell / membrane raft / fusion of virus membrane with host endosome membrane / viral envelope / lipid binding / host cell plasma membrane / virion membrane / extracellular region / identical protein binding
Similarity search - Function
Filoviruses glycoprotein, extracellular domain / Filoviruses glycoprotein / Filovirus glycoprotein
Similarity search - Domain/homology
Virion spike glycoprotein / Virion spike glycoprotein / Envelope glycoprotein
Similarity search - Component
Biological speciesZaire ebolavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsGilman, M.S.A. / Rutten, L. / Langedijk, J.P.M. / McLellan, J.S.
CitationJournal: Cell Rep / Year: 2020
Title: Structure-Based Design of Prefusion-Stabilized Filovirus Glycoprotein Trimers.
Authors: Rutten, L. / Gilman, M.S.A. / Blokland, S. / Juraszek, J. / McLellan, J.S. / Langedijk, J.P.M.
History
DepositionJan 21, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / 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_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 11, 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
A: Virion spike glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0923
Polymers55,4461
Non-polymers6462
Water0
1
A: Virion spike glycoprotein
hetero molecules

A: Virion spike glycoprotein
hetero molecules

A: Virion spike glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,2769
Polymers166,3393
Non-polymers1,9376
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area15030 Å2
ΔGint-35 kcal/mol
Surface area46260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.110, 113.110, 393.180
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Virion spike glycoprotein


Mass: 55446.449 Da / Num. of mol.: 1 / Mutation: T42A/T577P/K588F,deletion of residues 320-476
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zaire ebolavirus / Gene: GP / Cell line (production host): Expi293F / Production host: Homo sapiens (human)
References: UniProt: A0A2I4PEY8, UniProt: A0A0E3XL33, UniProt: Q05320*PLUS
#2: 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.: 1
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
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestN

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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: 4.36 Å3/Da / Density % sol: 71.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: 9.8% PEG 6000, 0.1 M Sodium citrate pH 5.2, 3% glycerol

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Oct 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.5→47.53 Å / Num. obs: 10491 / % possible obs: 84.7 % / Redundancy: 4.3 % / CC1/2: 0.913 / Rmerge(I) obs: 0.346 / Rpim(I) all: 0.177 / Rrim(I) all: 0.391 / Net I/σ(I): 3.4 / Num. measured all: 45250 / Scaling rejects: 3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3.5-3.834.30.7431098525270.5640.3780.838286.7
8.57-47.534.50.15632737270.9720.0760.174680.6

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
iMOSFLMdata reduction
PHASER2.5.7phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JQ3

5jq3


Resolution: 3.5→47.53 Å / SU ML: 0.53 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.89
RfactorNum. reflection% reflection
Rfree0.3031 525 5 %
Rwork0.2839 --
obs0.2849 10491 82.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 130.14 Å2 / Biso mean: 62.1766 Å2 / Biso min: 33.85 Å2
Refinement stepCycle: final / Resolution: 3.5→47.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2773 0 42 0 2815
Biso mean--64.79 --
Num. residues----353
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.5001-3.85220.33121210.3108251985
3.8522-4.40930.34621340.2822248284
4.4093-5.55390.27861320.2701248483
5.5539-47.530.27741380.2816248180
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)
11.89870.5159-0.07642.333-0.10092.3550.0078-0.2825-0.33550.1923-0.06130.0220.5194-0.14890.03970.47530.01910.0370.2660.01120.5117-3.319939.8087-40.4176
21.10150.2859-0.52772.17270.47881.8912-0.03320.1805-0.185-0.32440.07540.20750.2114-0.2691-0.04260.264-0.0188-0.08870.29950.05570.5156-3.247253.8682-61.8317
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 33:526)A33 - 526
2X-RAY DIFFRACTION2chain A and resid 527:620A527 - 620

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