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- PDB-6mam: Cleaved Ebola GP in complex with a broadly neutralizing human ant... -

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Basic information

Entry
Database: PDB / ID: 6mam
TitleCleaved Ebola GP in complex with a broadly neutralizing human antibody, ADI-15946
Components
  • (ADI-15946 Fab ...) x 2
  • (Envelope glycoprotein) x 2
KeywordsViral protein/immune system / Ebola / ebolavirus / antibody / mab / fab / GP / glycoprotein / cleaved / monoclonal / broad / filovirus / marburg / EBOV / BDBV / SUDV / RESTV / TAFV / MARV / RAVV / bundibugyo / sudan / human / VIRAL PROTEIN / Viral protein-immune system complex
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-mediated suppression of host innate immune response / 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 / symbiont-mediated suppression of host innate immune response / symbiont entry into host cell / membrane raft / fusion of virus membrane with host endosome membrane / lipid binding / viral envelope / 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
Envelope glycoprotein
Similarity search - Component
Biological speciesHomo sapiens (human)
Zaire ebolavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.1 Å
AuthorsWest, B.R. / Moyer, C.L. / Fusco, M.L. / Saphire, E.O.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19 AI09762-04 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI132204 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19 AI109711 United States
Defense Threat Reduction Agency (DTRA)HDTRA1-13-1-0034 United States
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2019
Title: Structural basis of broad ebolavirus neutralization by a human survivor antibody.
Authors: West, B.R. / Wec, A.Z. / Moyer, C.L. / Fusco, M.L. / Ilinykh, P.A. / Huang, K. / Wirchnianski, A.S. / James, R.M. / Herbert, A.S. / Hui, S. / Goodwin, E. / Howell, K.A. / Kailasan, S. / ...Authors: West, B.R. / Wec, A.Z. / Moyer, C.L. / Fusco, M.L. / Ilinykh, P.A. / Huang, K. / Wirchnianski, A.S. / James, R.M. / Herbert, A.S. / Hui, S. / Goodwin, E. / Howell, K.A. / Kailasan, S. / Aman, M.J. / Walker, L.M. / Dye, J.M. / Bukreyev, A. / Chandran, K. / Saphire, E.O.
History
DepositionAug 28, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
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_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 / 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
A: ADI-15946 Fab Heavy Chain
B: ADI-15946 Fab Light Chain
C: ADI-15946 Fab Heavy Chain
D: ADI-15946 Fab Light Chain
E: ADI-15946 Fab Heavy Chain
F: ADI-15946 Fab Light Chain
G: Envelope glycoprotein
H: Envelope glycoprotein
I: Envelope glycoprotein
J: Envelope glycoprotein
K: Envelope glycoprotein
L: Envelope glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)264,47315
Polymers261,90212
Non-polymers2,5703
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)182.273, 182.273, 262.012
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322

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Components

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Protein , 2 types, 6 molecules GIKHJL

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


Mass: 25275.326 Da / Num. of mol.: 3
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): S2 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q05320
#4: Protein Envelope glycoprotein / GP1 / 2 / GP


Mass: 12254.977 Da / Num. of mol.: 3
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): S2 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q05320

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Antibody , 2 types, 6 molecules ACEBDF

#1: Antibody ADI-15946 Fab Heavy Chain


Mass: 25977.000 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): S2 / Production host: Drosophila melanogaster (fruit fly)
#2: Antibody ADI-15946 Fab Light Chain


Mass: 23793.426 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): S2 / Production host: Drosophila melanogaster (fruit fly)

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Sugars , 2 types, 3 molecules

#5: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[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: 910.823 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#6: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}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: 4.15 Å3/Da / Density % sol: 70.39 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 8.2
Details: 0.2 M sodium citrate tribasic dihydrate, 20% polyethelyene glycol 3350

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 4.1→48.544 Å / Num. obs: 35312 / % possible obs: 99.6 % / Redundancy: 13.1 % / CC1/2: 1 / Net I/σ(I): 14.6
Reflection shellResolution: 4.1→4.3 Å / Redundancy: 13.4 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 3460 / CC1/2: 0.7 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5hj3

5hj3


Resolution: 4.1→48.544 Å / SU ML: 0.54 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.34
RfactorNum. reflection% reflection
Rfree0.281 1792 5.1 %
Rwork0.262 --
obs0.2684 35153 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 4.1→48.544 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16358 0 172 0 16530
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00216951
X-RAY DIFFRACTIONf_angle_d0.58723079
X-RAY DIFFRACTIONf_dihedral_angle_d15.06110086
X-RAY DIFFRACTIONf_chiral_restr0.0432605
X-RAY DIFFRACTIONf_plane_restr0.0032935
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.1-4.21080.34171270.3712531X-RAY DIFFRACTION100
4.2108-4.33460.35051320.33632533X-RAY DIFFRACTION100
4.3346-4.47450.31951400.30962522X-RAY DIFFRACTION100
4.4745-4.63430.30251180.30672543X-RAY DIFFRACTION100
4.6343-4.81960.29011520.30952518X-RAY DIFFRACTION100
4.8196-5.03880.30551450.30982544X-RAY DIFFRACTION100
5.0388-5.30410.3231270.2992551X-RAY DIFFRACTION100
5.3041-5.6360.33761490.30692535X-RAY DIFFRACTION100
5.636-6.07040.33171420.28782580X-RAY DIFFRACTION100
6.0704-6.67990.29451340.2912579X-RAY DIFFRACTION100
6.6799-7.64320.31741320.27352613X-RAY DIFFRACTION100
7.6432-9.61740.22131440.20192612X-RAY DIFFRACTION99
9.6174-48.54690.23021500.21052700X-RAY DIFFRACTION97

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