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- PDB-6p91: Structure of Lassa virus glycoprotein bound to Fab 18.5C -

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Basic information

Entry
Database: PDB / ID: 6p91
TitleStructure of Lassa virus glycoprotein bound to Fab 18.5C
Components
  • (Fab 18.5C Antibody ...) x 2
  • (Pre-glycoprotein polyprotein GP ...) x 2
Keywordsviral protein/immune system / Lassa virus / glycoprotein / antibody / VIRAL PROTEIN / viral protein-immune system complex
Function / homology
Function and homology information


host cell Golgi membrane / receptor-mediated endocytosis of virus by host cell / 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 / metal ion binding / membrane
Similarity search - Function
Arenavirus glycoprotein, zinc binding domain / Arenavirus glycoprotein / Arenavirus glycoprotein / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Pre-glycoprotein polyprotein GP complex / Pre-glycoprotein polyprotein GP complex
Similarity search - Component
Biological speciesLassa mammarenavirus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4 Å
AuthorsSaphire, E.O. / Hastie, K.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1U19-AI109762 United States
CitationJournal: Cell / Year: 2019
Title: Convergent Structures Illuminate Features for Germline Antibody Binding and Pan-Lassa Virus Neutralization.
Authors: Hastie, K.M. / Cross, R.W. / Harkins, S.S. / Zandonatti, M.A. / Koval, A.P. / Heinrich, M.L. / Rowland, M.M. / Robinson, J.E. / Geisbert, T.W. / Garry, R.F. / Branco, L.M. / Saphire, E.O.
History
DepositionJun 9, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Data collection / Category: chem_comp / pdbx_audit_support
Item: _chem_comp.type / _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_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 / _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
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pre-glycoprotein polyprotein GP complex
H: Fab 18.5C Antibody heavy chain
L: Fab 18.5C Antibody light chain
a: Pre-glycoprotein polyprotein GP complex,Lassa virus glycoprotein, GP2 subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,82014
Polymers99,4984
Non-polymers5,32210
Water00
1
A: Pre-glycoprotein polyprotein GP complex
H: Fab 18.5C Antibody heavy chain
L: Fab 18.5C Antibody light chain
a: Pre-glycoprotein polyprotein GP complex,Lassa virus glycoprotein, GP2 subunit
hetero molecules

A: Pre-glycoprotein polyprotein GP complex
H: Fab 18.5C Antibody heavy chain
L: Fab 18.5C Antibody light chain
a: Pre-glycoprotein polyprotein GP complex,Lassa virus glycoprotein, GP2 subunit
hetero molecules

A: Pre-glycoprotein polyprotein GP complex
H: Fab 18.5C Antibody heavy chain
L: Fab 18.5C Antibody light chain
a: Pre-glycoprotein polyprotein GP complex,Lassa virus glycoprotein, GP2 subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)314,46042
Polymers298,49412
Non-polymers15,96630
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_445z-1/2,-x-1/2,-y1
crystal symmetry operation12_455-y-1/2,-z,x+1/21
Buried area67840 Å2
ΔGint21 kcal/mol
Surface area99460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)231.660, 231.660, 231.660
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number199
Space group name H-MI213

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Components

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Pre-glycoprotein polyprotein GP ... , 2 types, 2 molecules Aa

#1: Protein Pre-glycoprotein polyprotein GP complex / Pre-GP-C


Mass: 28784.039 Da / Num. of mol.: 1 / Mutation: R207C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lassa mammarenavirus / Gene: GP, GPC / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q6GWS0, UniProt: P08669*PLUS
#4: Protein Pre-glycoprotein polyprotein GP complex,Lassa virus glycoprotein, GP2 subunit / Pre-GP-C


Mass: 22750.439 Da / Num. of mol.: 1 / Mutation: E329P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lassa mammarenavirus / Gene: GP, GPC / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q6GWS0, UniProt: P08669*PLUS

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Antibody , 2 types, 2 molecules HL

#2: Antibody Fab 18.5C Antibody heavy chain


Mass: 24309.412 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Antibody Fab 18.5C Antibody light chain


Mass: 23654.180 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)

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Sugars , 5 types, 10 molecules

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


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}}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

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Details

Has ligand of interestN
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: 5.37 Å3/Da / Density % sol: 77.11 % / Description: box-like
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 0.15-0.2 M ammonium sulfate, 0.1M Tris pH 5-8.5 / PH range: 5-8.5

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9796 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 3.79→49.37 Å / Num. obs: 20596 / % possible obs: 99.8 % / Redundancy: 19.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.201 / Rpim(I) all: 0.047 / Rrim(I) all: 0.207 / Net I/σ(I): 11
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3.79-4.1519.14.5029281748610.6151.0484.6250.999.5
9.29-49.3717.30.062529814660.9980.0150.06241.599.4

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VK2, 4FQL

5vk2

4fql


Resolution: 4→38.61 Å / SU ML: 0.59 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.3
RfactorNum. reflection% reflection
Rfree0.2539 850 4.84 %
Rwork0.2041 --
obs0.2065 17579 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 443.43 Å2 / Biso mean: 209.0791 Å2 / Biso min: 127.74 Å2
Refinement stepCycle: final / Resolution: 4→38.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6061 0 353 0 6414
Biso mean--270.25 --
Num. residues----780
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
4.0001-4.25040.36881470.29512721286899
4.2504-4.57810.24041230.198427912914100
4.5781-5.03790.22371530.17927552908100
5.0379-5.76490.24491250.173627962921100
5.7649-7.25520.26791700.230827752945100
7.2552-38.61180.24521320.199728913023100
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)
11.8869-0.7695-0.19952.47410.44921.94250.4615-0.16740.1256-0.038-0.266-0.3694-0.0260.4158-0.17641.5581-0.0061-0.09761.9222-0.11711.7957-42.928-46.77658.247
24.246-1.0828-0.93041.7431-1.47726.33410.10940.1277-0.4156-0.53510.0504-0.17870.1979-0.0895-0.14691.55290.10290.19161.733-0.19631.5898-39.693-43.16719.666
32.6047-0.793-1.44261.95570.21074.38730.4510.7710.0845-0.1435-0.017-0.0376-0.50230.1096-0.22961.90380.20770.19232.3504-0.13591.7549-21.482-45.539-9.97
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 60:254 )A60 - 254
2X-RAY DIFFRACTION2( CHAIN H AND RESID 2:128 ) OR ( CHAIN L AND RESID 1:126 )H2 - 128
3X-RAY DIFFRACTION2( CHAIN H AND RESID 2:128 ) OR ( CHAIN L AND RESID 1:126 )L1 - 126
4X-RAY DIFFRACTION3( CHAIN H AND RESID 129:229 ) OR ( CHAIN L AND RESID 127:232 )H129 - 229
5X-RAY DIFFRACTION3( CHAIN H AND RESID 129:229 ) OR ( CHAIN L AND RESID 127:232 )L127 - 232

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