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- PDB-6eay: Structural Basis for Broad Neutralization of Ebolaviruses by an A... -

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Basic information

Entry
Database: PDB / ID: 6eay
TitleStructural Basis for Broad Neutralization of Ebolaviruses by an Antibody Targeting the Glycoprotein Fusion Loop
Components
  • (Envelope glycoprotein) x 2
  • CA45 heavy chain
  • CA45 light chain
KeywordsVIRAL PROTEIN / ebolavirus / glycoprotein / cross-protective antibody / broadly neutralizing antibody / CA45 / fusion loop / cross-reactive / filovirus
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 / symbiont entry into host cell / membrane raft / fusion of virus membrane with host endosome membrane / viral envelope ...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 / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Envelope glycoprotein
Similarity search - Component
Biological speciesMacaca fascicularis (crab-eating macaque)
Zaire ebolavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.72 Å
AuthorsJanus, B.M. / Ofek, G.
CitationJournal: Nat Commun / Year: 2018
Title: Structural basis for broad neutralization of ebolaviruses by an antibody targeting the glycoprotein fusion loop.
Authors: Janus, B.M. / van Dyk, N. / Zhao, X. / A Howell, K. / Soto, C. / Aman, M.J. / Li, Y. / Fuerst, T.R. / Ofek, G.
History
DepositionAug 3, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2018Provider: 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 / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_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 / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: CA45 light chain
H: CA45 heavy chain
A: Envelope glycoprotein
B: Envelope glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,2577
Polymers102,4174
Non-polymers1,8403
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11850 Å2
ΔGint-31 kcal/mol
Surface area37000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.429, 153.429, 335.862
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

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Protein , 2 types, 2 molecules AB

#3: Protein Envelope glycoprotein / GP1 / 2 / GP


Mass: 18636.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zaire ebolavirus (strain Mayinga-76) / Strain: Mayinga-76 / Gene: GP / Cell line (production host): HEK293S GNTI-/- / Production host: Homo sapiens (human) / References: UniProt: Q05320
#4: Protein Envelope glycoprotein / GP1 / 2 / GP


Mass: 35319.570 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zaire ebolavirus (strain Mayinga-76) / Strain: Mayinga-76 / Gene: GP / Cell line (production host): HEK293S GNTI-/- / Production host: Homo sapiens (human) / References: UniProt: Q05320

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Antibody , 2 types, 2 molecules LH

#1: Antibody CA45 light chain


Mass: 23291.760 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca fascicularis (crab-eating macaque)
Cell: B cell / Cell line (production host): HEK 293F / Production host: Homo sapiens (human)
#2: Antibody CA45 heavy chain


Mass: 25169.197 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca fascicularis (crab-eating macaque)
Cell: B cell / Cell line (production host): HEK 293F / Production host: Homo sapiens (human)

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Sugars , 2 types, 3 molecules

#5: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1397.245 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3[DManpa1-3[DManpa1-6]DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,8,7/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1_f3-g1_f6-h1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#6: 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
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

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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: 3.71 Å3/Da / Density % sol: 73.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 1M Potassium Sodium Tartrate, 0.1M MES pH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Nov 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.72→76.71 Å / Num. obs: 14037 / % possible obs: 87.2 % / Redundancy: 9.8 % / CC1/2: 0.993 / Rmerge(I) obs: 0.181 / Rpim(I) all: 0.054 / Net I/σ(I): 9.9
Reflection shellResolution: 3.72→4.07 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.589 / Mean I/σ(I) obs: 3.9 / Num. unique obs: 1402 / CC1/2: 0.859 / Rpim(I) all: 0.176 / % possible all: 88.5

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Processing

Software
NameVersionClassification
PHENIX(1.14_3228: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JQ3, 3Q6G

5jq3

3q6g


Resolution: 3.72→45.128 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2966 695 4.96 %Random
Rwork0.2586 ---
obs0.2604 14025 85.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.72→45.128 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5254 0 122 0 5376
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025518
X-RAY DIFFRACTIONf_angle_d0.577583
X-RAY DIFFRACTIONf_dihedral_angle_d17.9011858
X-RAY DIFFRACTIONf_chiral_restr0.046899
X-RAY DIFFRACTIONf_plane_restr0.004966
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.7201-4.00720.34671380.33012656X-RAY DIFFRACTION87
4.0072-4.41020.23741470.26392690X-RAY DIFFRACTION88
4.4102-5.04760.26571480.24222645X-RAY DIFFRACTION86
5.0476-6.35660.37691100.27472687X-RAY DIFFRACTION85
6.3566-45.13150.29221520.23022652X-RAY DIFFRACTION83
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)
17.8275.87463.48065.84870.07658.0013-1.37551.6747-0.0065-1.57740.85991.7875-0.97580.95820.32961.4445-0.2878-0.05950.84690.00131.799729.6068-62.7008-54.9724
27.85615.13014.607610.19973.24636.1205-0.14030.3948-0.2381-0.41690.305-0.7246-0.13970.8638-0.20950.626-0.0228-0.10140.6334-0.07791.386533.9795-63.9597-46.0674
36.86694.9577-3.65936.2865-4.99518.822-0.76450.33550.9203-2.0510.16030.42160.92781.13170.52881.0673-0.2289-0.29380.86470.16961.747429.0615-60.6322-47.4949
45.97672.0104-0.06163.24591.35294.42560.7647-1.06480.77950.267-0.6231.0584-0.4316-0.052-0.16291.0407-0.21480.20190.8946-0.20982.56662.4508-70.2363-35.7268
57.3294-2.9152-0.72642.3527-1.22142.47680.8685-0.50870.338-0.7249-0.97644.30831.0717-1.45130.50150.4091-0.31710.84591.1735-0.65583.064-6.904-70.2824-32.7785
67.6656-6.5682-0.77045.91771.20885.2582-1.1829-0.66911.80490.82380.5361.403-0.5455-0.2850.5790.626-0.0296-0.26670.66370.00341.460630.6248-45.4169-30.6914
74.84444.2744-0.3783.7183-0.79992.8385-1.05240.0294-1.1286-0.15250.80580.6973-0.1375-0.08590.38290.7961-0.1778-0.34980.75490.27142.152529.2086-46.7591-41.8874
82.10561.3668-0.10481.694-0.73422.4863-0.41180.32680.5755-0.2562-0.34311.3382-0.67950.59680.47970.7533-0.301-0.33280.5087-0.05613.032532.1449-47.1664-38.2661
95.8554-4.03061.09122.6144-0.83581.81540.4907-0.73581.03541.6045-0.85750.10330.13250.00010.39321.2045-0.35950.07121.22-0.26932.09369.5037-59.3324-25.8737
108.0842-4.5945-1.10163.8733-2.89568.56310.9424-0.7239-0.2682-0.4869-0.9480.8308-0.00230.524-0.04151.094-0.2080.05071.08-0.10081.75287.9309-61.6136-22.6324
119.6810.15620.45995.76113.63579.0449-0.58950.6658-0.1243-1.4372-0.4246-0.246-0.5809-0.19590.86680.4204-0.1385-0.01710.7885-0.16011.523354.1872-58.5193-35.8214
125.9001-5.8998-0.86541.999-2.09031.82783.48332.0173-3.1659-2.0448-0.1825.18743.49441.8001-3.11111.20080.4166-0.19951.07730.15111.607951.7226-28.39-32.1063
132.845-0.3981-1.28343.99272.20254.07630.10290.0962-0.32070.5431-0.25960.33950.5252-0.39590.2110.4685-0.06890.01910.41920.12241.131959.1797-53.2033-32.4941
145.21931.5676-4.63485.0359-5.24377.8540.2507-0.81590.2287-0.65971.33121.13681.5052-0.1729-1.03980.4326-0.1869-0.03530.63230.23740.960175.1582-50.9146-38.4799
158.2198-2.0556-4.93035.3725.71867.15040.11822.2006-2.22331.5964-0.48081.79071.911-2.68840.6421.6742-0.13710.16371.6206-0.51952.235576.0115-50.3201-63.1621
161.9814-4.53567.9618.25860.11736.67371.06627.4046-0.4221-2.98760.02640.43980.63490.9358-0.56841.1513-0.0015-0.35891.5021-0.09640.959165.2416-60.0269-46.7422
172.05432.1347-2.22933.5432-2.47056.4425-0.20270.11440.14920.29480.57310.4397-0.0198-1.1143-0.29540.4864-0.0818-0.00030.51480.05491.351161.6212-60.3306-30.906
183.8568-1.44082.9673.1645-1.71027.973-0.3874-0.41960.12240.2770.1799-0.0781-0.8842-0.29020.19640.5062-0.017-0.06680.5241-0.08821.252164.7909-57.43-16.2361
193.99041.2803-5.64942.6422-0.25988.3391-0.3908-0.3791-0.46110.234-0.03430.21940.44080.12830.37040.3640.00080.04180.35240.0530.900963.2355-58.0129-19.7391
204.3869-3.26853.60592.2881-2.45833.2111-1.0381-2.72460.07381.43691.46110.4697-1.9519-0.6982-0.98290.6073-0.24610.29590.68850.09341.49250.6052-55.6845-16.2867
215.4405-0.18182.25049.9162-0.66271.6951-0.35590.7466-0.1931.3603-1.0526-2.45581.30060.32280.97460.6329-0.22690.23350.89970.17461.058752.9586-68.7567-5.5561
225.93165.31615.29799.99677.54716.25340.84581.9119-0.236-2.13411.42730.1557-1.67640.3111-1.34571.0553-0.2166-0.1162-0.01550.62232.068840.8507-64.1281-9.8468
235.7077-5.46220.05367.8441-4.7498.96540.4269-0.45240.9777-0.83260.43412.1080.747-0.8897-0.93560.68750.03280.29270.79540.40922.051841.8123-68.84660.9783
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'L' and (resid 2 through 33 )
2X-RAY DIFFRACTION2chain 'L' and (resid 34 through 75 )
3X-RAY DIFFRACTION3chain 'L' and (resid 76 through 102 )
4X-RAY DIFFRACTION4chain 'L' and (resid 103 through 172 )
5X-RAY DIFFRACTION5chain 'L' and (resid 173 through 212 )
6X-RAY DIFFRACTION6chain 'H' and (resid 2 through 33 )
7X-RAY DIFFRACTION7chain 'H' and (resid 34 through 52 )
8X-RAY DIFFRACTION8chain 'H' and (resid 73 through 113 )
9X-RAY DIFFRACTION9chain 'H' and (resid 114 through 169 )
10X-RAY DIFFRACTION10chain 'H' and (resid 170 through 208 )
11X-RAY DIFFRACTION11chain 'A' and (resid 502 through 524 )
12X-RAY DIFFRACTION12chain 'A' and (resid 525 through 529 )
13X-RAY DIFFRACTION13chain 'A' and (resid 530 through 575 )
14X-RAY DIFFRACTION14chain 'A' and (resid 576 through 596 )
15X-RAY DIFFRACTION15chain 'A' and (resid 597 through 614 )
16X-RAY DIFFRACTION16chain 'B' and (resid 32 through 50 )
17X-RAY DIFFRACTION17chain 'B' and (resid 51 through 89 )
18X-RAY DIFFRACTION18chain 'B' and (resid 90 through 126 )
19X-RAY DIFFRACTION19chain 'B' and (resid 127 through 185 )
20X-RAY DIFFRACTION20chain 'B' and (resid 186 through 223 )
21X-RAY DIFFRACTION21chain 'B' and (resid 224 through 249 )
22X-RAY DIFFRACTION22chain 'B' and (resid 250 through 260 )
23X-RAY DIFFRACTION23chain 'B' and (resid 261 through 280 )

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