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- PDB-6bp2: Therapeutic human monoclonal antibody MR191 bound to a marburgvir... -

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Basic information

Entry
Database: PDB / ID: 6bp2
TitleTherapeutic human monoclonal antibody MR191 bound to a marburgvirus glycoprotein
Components
  • Envelope glycoprotein
  • Envelope glycoprotein GP2
  • MR191 Fab Heavy Chain
  • MR191 Fab Light Chain
KeywordsVIRAL PROTEIN/immune system / Marburg / Ravn / Glycoprotein / Complex / VIRAL PROTEIN / VIRAL PROTEIN-immune system complex
Function / homology
Function and homology information


fusion of virus membrane with host endosome membrane / viral envelope / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane / virion membrane / membrane / plasma membrane
Similarity search - Function
TLV/ENV coat polyprotein / : / 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 / Envelope glycoprotein
Similarity search - Component
Biological speciesMarburg marburgvirus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.172 Å
AuthorsKing, L.B. / Fusco, M.L. / Flyak, A.I. / Ilinykh, P.A. / Huang, K. / Gunn, B. / Kirchdoerfer, R.N. / Hastie, K.M. / Sangha, A.K. / Meiler, J. ...King, L.B. / Fusco, M.L. / Flyak, A.I. / Ilinykh, P.A. / Huang, K. / Gunn, B. / Kirchdoerfer, R.N. / Hastie, K.M. / Sangha, A.K. / Meiler, J. / Alter, G. / Bukreyev, A. / Crowe, J.E.J. / Saphire, E.O.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI089498 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19AI109762 United States
CitationJournal: Cell Host Microbe / Year: 2018
Title: The Marburgvirus-Neutralizing Human Monoclonal Antibody MR191 Targets a Conserved Site to Block Virus Receptor Binding.
Authors: King, L.B. / Fusco, M.L. / Flyak, A.I. / Ilinykh, P.A. / Huang, K. / Gunn, B. / Kirchdoerfer, R.N. / Hastie, K.M. / Sangha, A.K. / Meiler, J. / Alter, G. / Bukreyev, A. / Crowe, J.E. / Saphire, E.O.
History
DepositionNov 21, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 2.0Mar 7, 2018Group: Advisory / Atomic model / Derived calculations
Category: atom_site / pdbx_unobs_or_zero_occ_atoms ...atom_site / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn / 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 / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_asym_id / _struct_site_gen.auth_comp_id / _struct_site_gen.auth_seq_id / _struct_site_gen.label_asym_id / _struct_site_gen.label_comp_id / _struct_site_gen.label_seq_id
Revision 2.1Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 3.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_asym / struct_conn / 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 / _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 / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _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 3.1Oct 4, 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
Revision 3.2Nov 13, 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
A: Envelope glycoprotein
B: Envelope glycoprotein GP2
H: MR191 Fab Heavy Chain
L: MR191 Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,6138
Polymers97,6734
Non-polymers1,9404
Water00
1
A: Envelope glycoprotein
B: Envelope glycoprotein GP2
H: MR191 Fab Heavy Chain
L: MR191 Fab Light Chain
hetero molecules

A: Envelope glycoprotein
B: Envelope glycoprotein GP2
H: MR191 Fab Heavy Chain
L: MR191 Fab Light Chain
hetero molecules

A: Envelope glycoprotein
B: Envelope glycoprotein GP2
H: MR191 Fab Heavy Chain
L: MR191 Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)298,83824
Polymers293,01912
Non-polymers5,81912
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_745-y+2,x-y-1,z1
crystal symmetry operation3_875-x+y+3,-x+2,z1
Buried area51380 Å2
ΔGint-172 kcal/mol
Surface area93880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.796, 133.796, 151.003
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Envelope glycoprotein


Mass: 27885.434 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Marburg marburgvirus / Gene: GP, DF49_53427gpGP / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: A0A0U2XLP5, UniProt: Q1PDC7*PLUS
#2: Protein Envelope glycoprotein GP2


Mass: 22560.977 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Marburg marburgvirus / Gene: GP, DF49_53427gpGP / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: A0A0U2XLP5, UniProt: Q1PDC7*PLUS

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Antibody , 2 types, 2 molecules HL

#3: Antibody MR191 Fab Heavy Chain


Mass: 24375.324 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Nicotiana benthamiana (plant)
#4: Antibody MR191 Fab Light Chain


Mass: 22851.213 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Nicotiana benthamiana (plant)

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Sugars , 3 types, 4 molecules

#5: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-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.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#6: 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
#7: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a1122h-1b_1-5][a1122h-1a_1-5]/1-2-2/a3-b1_a6-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}LINUCSPDB-CARE

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Details

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: 3.85 Å3/Da / Density % sol: 68.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100 mM HEPES pH 7.5, 5% PEG 3000, 26% PEG 400, 6% Glycerol
Temp details: Room temperature

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 3.17→46.17 Å / Num. obs: 26795 / % possible obs: 99.28 % / Redundancy: 11 % / CC1/2: 0.998 / Rmerge(I) obs: 0.16 / Rrim(I) all: 0.17 / Net I/σ(I): 12.4
Reflection shellResolution: 3.17→3.29 Å / Redundancy: 11.5 % / Rmerge(I) obs: 2.02 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2652 / % possible all: 98.38

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3X2D

3x2d
PDB Unreleased entry


Resolution: 3.172→46.167 Å / SU ML: 0.52 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2837 1361 5.09 %
Rwork0.252 --
obs0.2536 26728 99.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.172→46.167 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5556 0 128 0 5684
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0135830
X-RAY DIFFRACTIONf_angle_d1.6517938
X-RAY DIFFRACTIONf_dihedral_angle_d10.5172112
X-RAY DIFFRACTIONf_chiral_restr0.082929
X-RAY DIFFRACTIONf_plane_restr0.013997
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1718-3.28520.41281350.39162464X-RAY DIFFRACTION98
3.2852-3.41670.41081170.37342540X-RAY DIFFRACTION99
3.4167-3.57210.32891510.34252481X-RAY DIFFRACTION100
3.5721-3.76040.3631040.30912539X-RAY DIFFRACTION100
3.7604-3.99580.33731210.28072537X-RAY DIFFRACTION99
3.9958-4.30410.26981730.24632499X-RAY DIFFRACTION100
4.3041-4.73690.28541390.20922539X-RAY DIFFRACTION100
4.7369-5.42140.26611450.22732566X-RAY DIFFRACTION100
5.4214-6.82690.26911240.24042579X-RAY DIFFRACTION99
6.8269-46.17140.23371520.21352623X-RAY DIFFRACTION97

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