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- PDB-5vk2: Structural basis for antibody-mediated neutralization of Lassa virus -

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Basic information

Entry
Database: PDB / ID: 5vk2
TitleStructural basis for antibody-mediated neutralization of Lassa virus
Components
  • (Pre-glycoprotein polyprotein GP ...) x 2
  • Fab 37.7H heavy chain
  • Fab 37.7H light chain
KeywordsVIRAL PROTEIN/Immune system / Lassa / glycoprotein / arenavirus / antibody / 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 / membrane / metal ion binding
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
Similarity search - Component
Biological speciesLassa virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.201 Å
AuthorsHastie, K.M. / Zandonatti, M.A. / Kleinfelter, L.M. / Rowland, M.L. / Rowland, M.M. / Chandra, K. / Branco, L.M. / Robinson, J.E. / Garry, R.F. / Saphire, E.O.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1U19AI109762-01 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21 AI116112 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32 GM007491 United States
CitationJournal: Science / Year: 2017
Title: Structural basis for antibody-mediated neutralization of Lassa virus.
Authors: Hastie, K.M. / Zandonatti, M.A. / Kleinfelter, L.M. / Heinrich, M.L. / Rowland, M.M. / Chandran, K. / Branco, L.M. / Robinson, J.E. / Garry, R.F. / Saphire, E.O.
History
DepositionApr 20, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 11, 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 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: Pre-glycoprotein polyprotein GP complex
a: Pre-glycoprotein polyprotein GP complex
B: Pre-glycoprotein polyprotein GP complex
b: Pre-glycoprotein polyprotein GP complex
C: Pre-glycoprotein polyprotein GP complex
c: Pre-glycoprotein polyprotein GP complex
D: Fab 37.7H heavy chain
E: Fab 37.7H light chain
F: Fab 37.7H heavy chain
G: Fab 37.7H light chain
H: Fab 37.7H heavy chain
L: Fab 37.7H light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)299,80243
Polymers286,98312
Non-polymers12,81931
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area44540 Å2
ΔGint-231 kcal/mol
Surface area90470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.697, 152.697, 456.738
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

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Pre-glycoprotein polyprotein GP ... , 2 types, 6 molecules ABCabc

#1: Protein Pre-glycoprotein polyprotein GP complex


Mass: 29098.430 Da / Num. of mol.: 3 / Fragment: UNP residues 1-259
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lassa virus / Strain: Mouse/Sierra Leone/Josiah/1976 / Gene: GPC, GP-C / Production host: Drosophila (fruit flies) / References: UniProt: P08669
#2: Protein Pre-glycoprotein polyprotein GP complex


Mass: 19116.732 Da / Num. of mol.: 3 / Fragment: UNP residues 260-423
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lassa virus (strain Mouse/Sierra Leone/Josiah/1976)
Strain: Mouse/Sierra Leone/Josiah/1976 / Gene: GPC, GP-C / Production host: Drosophila (fruit flies) / References: UniProt: P08669

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Antibody , 2 types, 6 molecules DFHEGL

#3: Antibody Fab 37.7H heavy chain


Mass: 24342.318 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#4: Antibody Fab 37.7H light chain


Mass: 23103.527 Da / Num. of mol.: 3
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, 31 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.: 3 / Source method: obtained synthetically
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.: 11 / Source method: obtained synthetically
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)-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.: 3 / Source method: obtained synthetically
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 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 3 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 11 / Source method: obtained synthetically / 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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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 54.18 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M Tris pH 8, 15-18% PEG 3350 and 0.1M-0.3M magnesium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97969 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97969 Å / Relative weight: 1
ReflectionResolution: 3.2→49.6 Å / Num. obs: 52823 / % possible obs: 99.7 % / Redundancy: 12.9 % / CC1/2: 0.999 / Net I/σ(I): 16.17
Reflection shellResolution: 3.2→3.3 Å / Redundancy: 12.6 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 4465 / CC1/2: 0.574 / Rpim(I) all: 0.845 / % possible all: 99.5

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Processing

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

5ine


Resolution: 3.201→49.602 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 2.02 / Phase error: 22.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2313 2296 5.04 %
Rwork0.1886 --
obs0.1908 45526 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.201→49.602 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17829 0 843 0 18672
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00319161
X-RAY DIFFRACTIONf_angle_d0.61526109
X-RAY DIFFRACTIONf_dihedral_angle_d11.8611399
X-RAY DIFFRACTIONf_chiral_restr0.043069
X-RAY DIFFRACTIONf_plane_restr0.0033229
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2009-3.27050.3568770.2981621X-RAY DIFFRACTION53
3.2705-3.34650.3081980.27651721X-RAY DIFFRACTION56
3.3465-3.43020.32581090.25552036X-RAY DIFFRACTION67
3.4302-3.52290.32231220.22772437X-RAY DIFFRACTION78
3.5229-3.62650.2811340.22532524X-RAY DIFFRACTION82
3.6265-3.74360.28211430.22042630X-RAY DIFFRACTION85
3.7436-3.87730.24541390.2122688X-RAY DIFFRACTION87
3.8773-4.03250.22051370.19732834X-RAY DIFFRACTION90
4.0325-4.21590.23061550.17872786X-RAY DIFFRACTION90
4.2159-4.43810.21581410.15753045X-RAY DIFFRACTION97
4.4381-4.71590.21531650.15123047X-RAY DIFFRACTION97
4.7159-5.07970.18481580.15073102X-RAY DIFFRACTION98
5.0797-5.59030.18761900.16233008X-RAY DIFFRACTION96
5.5903-6.39770.22531700.19053156X-RAY DIFFRACTION98
6.3977-8.05490.25671740.20013175X-RAY DIFFRACTION98
8.0549-49.60810.22281840.19393420X-RAY DIFFRACTION99
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)
12.2568-0.29210.22741.18010.18520.7158-0.08230.0552-0.25730.13590.06890.11240.1652-0.07900.56370.13760.00660.45440.0060.6953-42.81918.42418.97
21.45410.96020.05491.13330.00050.4562-0.22830.15370.07160.19850.10410.11230.0537-0.093500.60680.02570.03540.9843-0.12670.6066-111.32834.41816.139
30.7279-0.2336-0.02551.889-0.33090.819-0.1174-0.04850.00580.1377-0.07130.0509-0.2272-0.0787-0.0010.66650.1145-0.13870.42060.00310.501-62.74185.00124.053
40.5284-0.8165-1.23111.0855-0.37711.2367-0.21260.1912-0.37380.23110.0098-0.07870.1544-0.0289-0.00130.65460.0609-0.16270.53940.110.8184-18.549-3.1420.525
51.40130.52170.76820.21770.07251.2555-0.0836-0.2723-0.0597-0.10130.3531-0.048-0.2159-0.0902-00.65240.00160.22390.75120.06490.525-142.66425.89313.745
60.75890.01690.49341.04540.29161.7764-0.05920.2493-0.1417-0.05020.0993-0.0395-0.16010.1097-00.46280.0643-0.01780.5286-0.02140.4628-54.22455.7420.247
71.70090.5055-0.24381.09190.35590.9917-0.11860.0330.4525-0.0237-0.13370.1086-0.2055-0.2491-0.23840.4590.0489-0.20790.5612-0.11390.5738-86.48958.543-0.571
80.9544-0.37280.02521.2367-0.36780.9008-0.0180.1294-0.3496-0.1408-0.15370.34620.1451-0.1647-00.48550.0348-0.07220.698-0.24160.7995-72.8829.005-2.678
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN E AND RESID 3:111 ) OR ( CHAIN D AND RESID 2:123 )E3 - 111
2X-RAY DIFFRACTION1( CHAIN E AND RESID 3:111 ) OR ( CHAIN D AND RESID 2:123 )D2 - 123
3X-RAY DIFFRACTION2( CHAIN G AND RESID 3:111 ) OR ( CHAIN F AND RESID 2:123 )G3 - 111
4X-RAY DIFFRACTION2( CHAIN G AND RESID 3:111 ) OR ( CHAIN F AND RESID 2:123 )F2 - 123
5X-RAY DIFFRACTION3( CHAIN H AND RESID 2:123 ) OR ( CHAIN L AND RESID 2:111 )H2 - 123
6X-RAY DIFFRACTION3( CHAIN H AND RESID 2:123 ) OR ( CHAIN L AND RESID 2:111 )L2 - 111
7X-RAY DIFFRACTION4( CHAIN E AND RESID 112:212 ) OR ( CHAIN D AND RESID 124:226 )E112 - 212
8X-RAY DIFFRACTION4( CHAIN E AND RESID 112:212 ) OR ( CHAIN D AND RESID 124:226 )D124 - 226
9X-RAY DIFFRACTION5( CHAIN G AND RESID 112:213 ) OR ( CHAIN F AND RESID 124:225 )G112 - 213
10X-RAY DIFFRACTION5( CHAIN G AND RESID 112:213 ) OR ( CHAIN F AND RESID 124:225 )F124 - 225
11X-RAY DIFFRACTION6( CHAIN A AND RESID 59:255 ) OR ( CHAIN a AND RESID 260:416 )A59 - 255
12X-RAY DIFFRACTION6( CHAIN A AND RESID 59:255 ) OR ( CHAIN a AND RESID 260:416 )a260 - 416
13X-RAY DIFFRACTION7( CHAIN B AND RESID 59:255 ) OR ( CHAIN b AND RESID 260:418 )B59 - 255
14X-RAY DIFFRACTION7( CHAIN B AND RESID 59:255 ) OR ( CHAIN b AND RESID 260:418 )b260 - 418
15X-RAY DIFFRACTION8( CHAIN C AND RESID 59:255 ) OR ( CHAIN c AND RESID 260:418 )C59 - 255
16X-RAY DIFFRACTION8( CHAIN C AND RESID 59:255 ) OR ( CHAIN c AND RESID 260:418 )c260 - 418

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