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- PDB-5uqy: Crystal structure of Marburg virus GP in complex with the human s... -

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Basic information

Entry
Database: PDB / ID: 5uqy
TitleCrystal structure of Marburg virus GP in complex with the human survivor antibody MR78
Components
  • (ENVELOPE GLYCOPROTEIN ...) x 2
  • MR78 Fab heavy chain
  • MR78 Fab light chain
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / glycoprotein / viral protein / antibody / Fab / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


symbiont entry into host cell / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
TLV/ENV coat polyprotein / Filoviruses glycoprotein, extracellular domain / Filoviruses glycoprotein / Filovirus glycoprotein / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
alpha-D-mannopyranose / Envelope glycoprotein
Similarity search - Component
Biological speciesLake Victoria marburgvirus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsHashiguchi, T. / Fusco, M.L. / Hastie, K.M. / Bomholdt, Z.A. / Lee, J.E. / Flyak, A.I. / Matsuoka, R. / Kohda, D. / Yanagi, Y. / Hammel, M. ...Hashiguchi, T. / Fusco, M.L. / Hastie, K.M. / Bomholdt, Z.A. / Lee, J.E. / Flyak, A.I. / Matsuoka, R. / Kohda, D. / Yanagi, Y. / Hammel, M. / Crowe, J.E. / Saphire, E.O.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19 AI109762 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI089498 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21AI069347 United States
CitationJournal: Cell / Year: 2015
Title: Structural basis for Marburg virus neutralization by a cross-reactive human antibody.
Authors: Hashiguchi, T. / Fusco, M.L. / Bornholdt, Z.A. / Lee, J.E. / Flyak, A.I. / Matsuoka, R. / Kohda, D. / Yanagi, Y. / Hammel, M. / Crowe, J.E. / Saphire, E.O.
History
DepositionFeb 8, 2017Deposition site: RCSB / Processing site: RCSB
SupersessionMar 1, 2017ID: 3X2D
Revision 1.0Mar 1, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Data collection / Category: diffrn_source / pdbx_audit_support
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 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 / 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_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _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 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ENVELOPE GLYCOPROTEIN GP1
B: ENVELOPE GLYCOPROTEIN GP2
C: MR78 Fab light chain
D: MR78 Fab heavy chain
E: ENVELOPE GLYCOPROTEIN GP1
F: ENVELOPE GLYCOPROTEIN GP2
G: MR78 Fab light chain
H: MR78 Fab heavy chain
I: ENVELOPE GLYCOPROTEIN GP1
J: ENVELOPE GLYCOPROTEIN GP2
K: MR78 Fab light chain
L: MR78 Fab heavy chain
M: ENVELOPE GLYCOPROTEIN GP1
N: ENVELOPE GLYCOPROTEIN GP2
O: MR78 Fab light chain
P: MR78 Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)412,48430
Polymers404,80216
Non-polymers7,68214
Water00
1
A: ENVELOPE GLYCOPROTEIN GP1
B: ENVELOPE GLYCOPROTEIN GP2
C: MR78 Fab light chain
D: MR78 Fab heavy chain
hetero molecules

A: ENVELOPE GLYCOPROTEIN GP1
B: ENVELOPE GLYCOPROTEIN GP2
C: MR78 Fab light chain
D: MR78 Fab heavy chain
hetero molecules

A: ENVELOPE GLYCOPROTEIN GP1
B: ENVELOPE GLYCOPROTEIN GP2
C: MR78 Fab light chain
D: MR78 Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)309,36721
Polymers303,60212
Non-polymers5,7659
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area42380 Å2
ΔGint-279 kcal/mol
Surface area88850 Å2
MethodPISA
2
E: ENVELOPE GLYCOPROTEIN GP1
F: ENVELOPE GLYCOPROTEIN GP2
G: MR78 Fab light chain
H: MR78 Fab heavy chain
I: ENVELOPE GLYCOPROTEIN GP1
J: ENVELOPE GLYCOPROTEIN GP2
K: MR78 Fab light chain
L: MR78 Fab heavy chain
M: ENVELOPE GLYCOPROTEIN GP1
N: ENVELOPE GLYCOPROTEIN GP2
O: MR78 Fab light chain
P: MR78 Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)309,36223
Polymers303,60212
Non-polymers5,76011
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area39180 Å2
ΔGint-244 kcal/mol
Surface area83470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)204.653, 204.653, 192.963
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

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ENVELOPE GLYCOPROTEIN ... , 2 types, 8 molecules AEIMBFJN

#1: Protein
ENVELOPE GLYCOPROTEIN GP1 / GP1 / 2 / GP / Virion spike glycoprotein


Mass: 27885.434 Da / Num. of mol.: 4 / Fragment: UNP residues 17-256, 426-435
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lake Victoria marburgvirus (strain Ravn-87)
Strain: Ravn-87 / Gene: GP / Plasmid: pMT / Cell line (production host): S2 / Production host: Drosophila (fruit flies) / References: UniProt: Q1PDC7
#2: Protein
ENVELOPE GLYCOPROTEIN GP2 / GP1 / 2 / GP / Virion spike glycoprotein


Mass: 26137.631 Da / Num. of mol.: 4 / Fragment: UNP residues 436-637
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lake Victoria marburgvirus (strain Ravn-87)
Strain: Ravn-87 / Gene: GP / Plasmid: pMT / Cell line (production host): S2 / Production host: Drosophila (fruit flies) / References: UniProt: Q1PDC7

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Antibody , 2 types, 8 molecules CGKODHLP

#3: Antibody
MR78 Fab light chain


Mass: 23307.877 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell: Hybridoma / Plasmid details: B cell hybrdoma
#4: Antibody
MR78 Fab heavy chain


Mass: 23869.578 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell: Hybridoma / Plasmid details: B cell hybrdoma

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Sugars , 6 types, 14 molecules

#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.: 6
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
#6: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D- ...alpha-D-mannopyranose-(1-2)-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: 1072.964 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1WURCSPDB2Glycan 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]{}}}}}LINUCSPDB-CARE
#7: 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.: 2
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
#8: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-2)-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: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-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_d2-e1WURCSPDB2Glycan 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]{}}}}}}LINUCSPDB-CARE
#9: 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.: 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
#10: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG 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: 2.88 Å3/Da / Density % sol: 57.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M NaCl, 0.05 M MES pH6.5, 13 % PEG4000, 0.5 % ethyl acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3.6→130.53 Å / Num. obs: 52806 / % possible obs: 99.4 % / Redundancy: 5.1 % / CC1/2: 0.994 / Rsym value: 0.144 / Net I/σ(I): 12.9
Reflection shellResolution: 3.6→3.612 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 534 / Rsym value: 0.94 / % 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: 3CSY

3csy


Resolution: 3.6→84.739 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.52
RfactorNum. reflection% reflection
Rfree0.262 2674 5.07 %
Rwork0.2212 --
obs0.2233 52782 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.6→84.739 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20699 0 509 0 21208
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00221750
X-RAY DIFFRACTIONf_angle_d0.53229644
X-RAY DIFFRACTIONf_dihedral_angle_d12.03112976
X-RAY DIFFRACTIONf_chiral_restr0.0393453
X-RAY DIFFRACTIONf_plane_restr0.0043690
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6004-3.66580.33771370.31142635X-RAY DIFFRACTION100
3.6658-3.73640.33671470.30182650X-RAY DIFFRACTION100
3.7364-3.81260.36661540.27522617X-RAY DIFFRACTION100
3.8126-3.89550.28341380.26512613X-RAY DIFFRACTION100
3.8955-3.98610.29341510.25222621X-RAY DIFFRACTION100
3.9861-4.08580.29141290.24882656X-RAY DIFFRACTION100
4.0858-4.19630.29411360.23382644X-RAY DIFFRACTION99
4.1963-4.31980.32231460.23612619X-RAY DIFFRACTION100
4.3198-4.45920.23961360.21632643X-RAY DIFFRACTION100
4.4592-4.61860.26371340.21782641X-RAY DIFFRACTION100
4.6186-4.80350.22981290.20452667X-RAY DIFFRACTION100
4.8035-5.0220.26051430.2132621X-RAY DIFFRACTION99
5.022-5.28680.25761390.21412622X-RAY DIFFRACTION100
5.2868-5.6180.26741550.20182647X-RAY DIFFRACTION100
5.618-6.05160.2581460.2042636X-RAY DIFFRACTION99
6.0516-6.66040.21821480.20162629X-RAY DIFFRACTION99
6.6604-7.62360.25831410.20472652X-RAY DIFFRACTION99
7.6236-9.60280.18031260.18942640X-RAY DIFFRACTION99
9.6028-84.76270.25471390.21372655X-RAY DIFFRACTION97

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