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- PDB-4zjf: Crystal structure of GP1 - the receptor binding domain of Lassa virus -

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Basic information

Entry
Database: PDB / ID: 4zjf
TitleCrystal structure of GP1 - the receptor binding domain of Lassa virus
ComponentsGlycoprotein
KeywordsVIRAL PROTEIN / Arenaviruse / Lassa / receptor binding / glycoprotein
Function / homology
Function and homology information


host cell Golgi membrane / receptor-mediated endocytosis of virus by host cell / membrane => GO:0016020 / host cell endoplasmic reticulum membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / membrane / metal ion binding
Similarity search - Function
Arenavirus glycoprotein, zinc binding domain / Arenavirus glycoprotein / Arenavirus glycoprotein
Similarity search - Domain/homology
Pre-glycoprotein polyprotein GP complex / Pre-glycoprotein polyprotein GP complex
Similarity search - Component
Biological speciesLassa virus Josiah
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.595 Å
AuthorsCohen-Dvashi, H. / Cohen, N. / Israeli, H. / Diskin, R.
CitationJournal: J Virol / Year: 2015
Title: Molecular Mechanism for LAMP1 Recognition by Lassa Virus.
Authors: Hadas Cohen-Dvashi / Nadav Cohen / Hadar Israeli / Ron Diskin /
Abstract: Lassa virus is a notorious human pathogen that infects many thousands of people each year in West Africa, causing severe viral hemorrhagic fevers and significant mortality. The surface glycoprotein ...Lassa virus is a notorious human pathogen that infects many thousands of people each year in West Africa, causing severe viral hemorrhagic fevers and significant mortality. The surface glycoprotein of Lassa virus mediates receptor recognition through its GP1 subunit. Here we report the crystal structure of GP1 from Lassa virus, which is the first representative GP1 structure for Old World arenaviruses. We identify a unique triad of histidines that forms a binding site for LAMP1, a known lysosomal protein recently discovered to be a critical receptor for internalized Lassa virus at acidic pH. We demonstrate that mutation of this histidine triad, which is highly conserved among Old World arenaviruses, impairs LAMP1 recognition. Our biochemical and structural data further suggest that GP1 from Lassa virus may undergo irreversible conformational changes that could serve as an immunological decoy mechanism. Together with a variable region that we identify on the surface of GP1, those could be two distinct mechanisms that Lassa virus utilizes to avoid antibody-based immune response.
IMPORTANCE: Structural data at atomic resolution for viral proteins is key for understanding their function at the molecular level and can facilitate novel avenues for combating viral infections. ...IMPORTANCE: Structural data at atomic resolution for viral proteins is key for understanding their function at the molecular level and can facilitate novel avenues for combating viral infections. Here we used X-ray protein crystallography to decipher the crystal structure of the receptor-binding domain (GP1) from Lassa virus. This is a pathogenic virus that causes significant illness and mortality in West Africa. This structure reveals the overall architecture of GP1 domains from the group of viruses known as the Old World arenaviruses. Using this structural information, we elucidated the mechanisms for pH switch and binding of Lassa virus to LAMP1, a recently identified host receptor that is critical for successful infection. Lastly, our structural analysis suggests two novel immune evasion mechanisms that Lassa virus may utilize to escape antibody-based immune response.
History
DepositionApr 29, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 27, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2015Group: Database references
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_validate_close_contact / 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_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycoprotein
B: Glycoprotein
C: Glycoprotein
D: Glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,83518
Polymers77,5194
Non-polymers4,31614
Water1,53185
1
A: Glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6715
Polymers19,3801
Non-polymers1,2914
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6715
Polymers19,3801
Non-polymers1,2914
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8223
Polymers19,3801
Non-polymers4422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6715
Polymers19,3801
Non-polymers1,2914
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.620, 86.470, 109.480
Angle α, β, γ (deg.)90.00, 92.81, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Glycoprotein /


Mass: 19379.693 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lassa virus Josiah / Gene: GPC / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A097F5U5, UniProt: P08669*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.: 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
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 8
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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.03 Å3/Da / Density % sol: 59.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M BisTris pH 5.0, 0.2 M ammonium acetate pH 7.0, 22 % (w/v) PEG 6000 and 5 % (v/v) PEG 200

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.953 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jul 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953 Å / Relative weight: 1
ReflectionResolution: 2.595→49.6 Å / Num. obs: 28667 / % possible obs: 99.1 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 14.3
Reflection shellResolution: 2.59→2.68 Å / Rmerge(I) obs: 1.139 / Mean I/σ(I) obs: 1.6 / % possible all: 94.2

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Processing

Software
NameVersionClassification
PHENIX1.9_1683refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.595→49.56 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2413 2006 8.35 %
Rwork0.2094 --
obs0.2121 24011 83.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.595→49.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4994 0 280 85 5359
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045430
X-RAY DIFFRACTIONf_angle_d0.8627384
X-RAY DIFFRACTIONf_dihedral_angle_d11.0631864
X-RAY DIFFRACTIONf_chiral_restr0.04852
X-RAY DIFFRACTIONf_plane_restr0.002928
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5953-2.66020.3245380.3078432X-RAY DIFFRACTION23
2.6602-2.73220.3649730.2912811X-RAY DIFFRACTION43
2.7322-2.81250.37661020.27541041X-RAY DIFFRACTION56
2.8125-2.90330.31791150.28041294X-RAY DIFFRACTION69
2.9033-3.00710.2861420.28341551X-RAY DIFFRACTION83
3.0071-3.12740.2621650.27331815X-RAY DIFFRACTION95
3.1274-3.26980.33341610.25681846X-RAY DIFFRACTION100
3.2698-3.44210.28021740.23681865X-RAY DIFFRACTION100
3.4421-3.65770.22871680.20841885X-RAY DIFFRACTION100
3.6577-3.940.21891670.18931876X-RAY DIFFRACTION100
3.94-4.33630.21141790.17031872X-RAY DIFFRACTION100
4.3363-4.96330.19221700.15021902X-RAY DIFFRACTION100
4.9633-6.25120.23281720.19611899X-RAY DIFFRACTION100
6.2512-49.56940.22381800.21171916X-RAY DIFFRACTION100

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