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- PDB-4dag: Structure of the Human Metapneumovirus Fusion Protein with Neutra... -

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Basic information

Entry
Database: PDB / ID: 4dag
TitleStructure of the Human Metapneumovirus Fusion Protein with Neutralizing Antibody Identifies a Pneumovirus Antigenic Site
Components
  • Fusion glycoprotein F0
  • Neutralizing Antibody DS7 heavy chain
  • Neutralizing Antibody DS7 light chain
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / viral protein / MPV fusion protein / antibody / immune system / DS7 antibody structure / DS7 / FAB structure / vaccine / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


complement-dependent cytotoxicity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin complex, circulating / IgG immunoglobulin complex / immunoglobulin receptor binding / FCGR activation / Role of phospholipids in phagocytosis ...complement-dependent cytotoxicity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin complex, circulating / IgG immunoglobulin complex / immunoglobulin receptor binding / FCGR activation / Role of phospholipids in phagocytosis / complement activation, classical pathway / antigen binding / FCGR3A-mediated IL10 synthesis / Regulation of Complement cascade / FCGR3A-mediated phagocytosis / B cell receptor signaling pathway / Regulation of actin dynamics for phagocytic cup formation / antibacterial humoral response / blood microparticle / Interleukin-4 and Interleukin-13 signaling / adaptive immune response / fusion of virus membrane with host plasma membrane / host cell plasma membrane / virion membrane / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0 / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type ...Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0 / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Fusion glycoprotein F0 / Immunoglobulin heavy constant gamma 1 / IGL@ protein
Similarity search - Component
Biological speciesHuman metapneumovirus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 3.3904 Å
AuthorsJardetzky, T.S. / Wen, X.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2012
Title: Structure of the human metapneumovirus fusion protein with neutralizing antibody identifies a pneumovirus antigenic site.
Authors: Wen, X. / Krause, J.C. / Leser, G.P. / Cox, R.G. / Lamb, R.A. / Williams, J.V. / Crowe, J.E. / Jardetzky, T.S.
History
DepositionJan 12, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 29, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2012Group: Database references
Revision 1.2Apr 18, 2012Group: Database references
Revision 1.3Aug 2, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / 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_ref_seq / struct_ref_seq_dif / 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_struct_assembly_gen.asym_id_list / _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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fusion glycoprotein F0
H: Neutralizing Antibody DS7 heavy chain
L: Neutralizing Antibody DS7 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,4155
Polymers90,5933
Non-polymers1,8222
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7000 Å2
ΔGint-7 kcal/mol
Surface area40930 Å2
MethodPISA
2
A: Fusion glycoprotein F0
H: Neutralizing Antibody DS7 heavy chain
L: Neutralizing Antibody DS7 light chain
hetero molecules

A: Fusion glycoprotein F0
H: Neutralizing Antibody DS7 heavy chain
L: Neutralizing Antibody DS7 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,82910
Polymers181,1866
Non-polymers3,6434
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_555-x,-x+y,-z1
Buried area16590 Å2
ΔGint-29 kcal/mol
Surface area79270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)258.96, 258.96, 167.36
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
DetailsDS7 heavy chain H residues 1-220 / DS7 lambda chain L residues 21-232

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Components

#1: Protein Fusion glycoprotein F0


Mass: 44946.223 Da / Num. of mol.: 1 / Mutation: Domains I, II and III
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human metapneumovirus / Plasmid: pcDNA3.1-F plasmid / Cell line (production host): HEK-293 / Production host: Homo sapiens (human) / References: UniProt: G3KCK8
#2: Antibody Neutralizing Antibody DS7 heavy chain


Mass: 23109.014 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGHG1 / Plasmid: pcDNA3.1-F plasmid / Cell line (production host): HEK-293 / Production host: Homo sapiens (human) / References: UniProt: P01857
#3: Antibody Neutralizing Antibody DS7 light chain


Mass: 22537.848 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGL@ / Plasmid: pcDNA3.1-F plasmid / Cell line (production host): HEK-293 / Production host: Homo sapiens (human) / References: UniProt: Q8N5F4
#4: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-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: 910.823 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-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_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE

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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

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 16% PEG 5000 MME, 15% Glycerol, 100 mM Citrate pH 5.6. Crystals appeared after 7-15 days with two distinct morphologies: a square-like crystal and a longer, pointed crystal form., VAPOR ...Details: 16% PEG 5000 MME, 15% Glycerol, 100 mM Citrate pH 5.6. Crystals appeared after 7-15 days with two distinct morphologies: a square-like crystal and a longer, pointed crystal form., VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 112 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 1, 2008
RadiationMonochromator: Double flat crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→224 Å / Num. all: 50076 / Num. obs: 36420 / % possible obs: 72.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Rmerge(I) obs: 0.179

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHARPphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MIR
Starting model: B20-4 Fab model, PDB ENTRY 2FJH

2fjh


Resolution: 3.3904→44.853 Å / SU ML: 0.84 / Isotropic thermal model: Isotropic
Cross valid method: Coot; Phenix and RCSB PDB Data Validation
σ(F): 0 / Phase error: 26.64 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2895 1855 5.1 %Random
Rwork0.2598 ---
all0.2613 50076 --
obs0.2613 36404 78.79 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 28.702 Å2 / ksol: 0.291 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--10.0449 Å20 Å20 Å2
2---10.0449 Å2-0 Å2
3---20.0898 Å2
Refinement stepCycle: LAST / Resolution: 3.3904→44.853 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5942 0 122 0 6064
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0116201
X-RAY DIFFRACTIONf_angle_d1.6748459
X-RAY DIFFRACTIONf_dihedral_angle_d21.7582138
X-RAY DIFFRACTIONf_chiral_restr0.0971031
X-RAY DIFFRACTIONf_plane_restr0.0081062
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3904-3.48210.5115170.4374226X-RAY DIFFRACTION7
3.4821-3.58450.461390.3794596X-RAY DIFFRACTION18
3.5845-3.70010.3041710.35141149X-RAY DIFFRACTION35
3.7001-3.83230.3451050.33622128X-RAY DIFFRACTION64
3.8323-3.98570.32671980.31353298X-RAY DIFFRACTION99
3.9857-4.16690.31221740.28543324X-RAY DIFFRACTION100
4.1669-4.38650.2511780.2473311X-RAY DIFFRACTION100
4.3865-4.6610.24351750.22773342X-RAY DIFFRACTION100
4.661-5.02050.25151590.21963360X-RAY DIFFRACTION99
5.0205-5.52490.27581960.23843365X-RAY DIFFRACTION100
5.5249-6.32240.35591780.26573401X-RAY DIFFRACTION100
6.3224-7.95830.28811920.25873430X-RAY DIFFRACTION100
7.9583-44.85710.27121730.24083619X-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)
14.90590.0385-1.10890.2571-0.05030.8975-0.0947-0.96210.17690.0222-0.0908-0.56120.01551.07370.05630.5221-0.2576-0.05441.9083-0.01880.5707-27.386115.1749-4.1543
20.80770.6115-1.15892.71530.91795.46350.4723-0.43770.49550.6452-0.2478-0.4831-0.86360.5929-0.11160.7718-0.23320.0772.32660.19270.93093.7017117.2075-25.6492
31.8406-0.4845-1.12411.06420.480.60050.0621-0.1418-0.32670.10950.2443-0.64620.34490.96510.00970.3602-0.35760.17552.99040.12840.9247-3.0722109.3912-15.8382
41.50770.50260.3152.6549-0.21613.4437-0.4729-0.23450.3080.2561-0.0583-0.1432-0.44050.71080.29250.6618-0.40140.041.6246-0.06090.6145-40.0832128.5438-2.628
55.3885-1.8752-2.16312.51982.5482.6371-0.2183-0.25410.31350.2136-0.1054-0.5296-0.35511.07520.08580.8104-0.46480.0432.0272-0.05430.5587-27.1888120.4279-1.0831
62.28420.9241.77271.52911.68044.15090.03550.06970.63730.1004-0.05750.2462-1.00430.29140.22720.5291-0.5466-0.36321.4772-0.11650.0968-46.8546125.3679-9.9288
75.22550.87360.62743.28150.22495.6055-0.03150.2514-0.0519-0.1814-0.0316-0.63980.1220.79490.0590.5904-0.4455-0.31921.5388-0.05010.2999-45.3628117.1043-16.5084
83.57291.3414-1.86652.7144-0.56451.9225-0.0407-0.81140.2860.17670.1318-0.2275-1.22640.4052-0.1237-0.3954-0.9590.03881.1951-0.10050.3467-52.0292114.791121.4105
96.2220.63780.51363.0399-0.09427.15520.2007-1.2884-1.3171.34080.08850.50361.3315-0.3138-0.2890.9785-0.6388-0.02441.09080.19170.4637-64.105191.171944.4523
105.4765-0.60511.02529.5974-2.10835.748-0.0303-0.271-0.12080.4789-0.3305-0.54420.40830.85640.07670.3867-0.7231-0.03361.05330.00660.5737-58.482998.921340.2823
112.0031-4.33016.37728.1059-2.62548.38650.36480.2396-0.4839-0.0447-0.04240.04540.3260.3159-0.0590.6761-0.75120.13720.87120.00590.5624-63.583493.879835.7809
125.3564-0.4066-0.28024.0522.04794.30530.3261-1.0622-0.45821.4336-0.431-1.02470.87250.70270.02770.8651-0.4016-0.18031.16890.12690.8238-56.196594.215848.0385
134.64-0.0401-0.18087.4523-0.99786.2243-0.39830.3864-0.065-1.31490.37020.23470.7970.62510.12870.6616-0.42610.16921.1118-0.07550.3779-50.636596.94163.8955
146.7441.5029-2.30695.67891.12641.5394-0.0261-0.7573-0.03450.40330.106-0.08490.30231.12560.0597-0.0562-0.6110.34341.04630.14490.5551-47.303398.822617.0394
152.2109-0.1698-1.39474.5027-1.45965.7519-0.3138-0.2244-0.175-0.350.0731-0.74170.7911.5170.28990.6438-0.2870.17321.1483-0.17370.5045-44.532797.9019.6709
162.91710.2662-2.36780.7596-1.93775.1237-0.1589-0.3171-0.36220.5758-0.2651-0.09651.10780.15640.37161.0236-0.85950.42950.88680.13120.7009-65.020585.960235.0687
175.5044-1.2914-4.15031.13581.75117.987-0.44840.2261-1.14160.0812-0.13680.19650.8642-0.94980.71171.4481-0.68420.08291.1497-0.1750.8257-72.340481.785431.689
183.8594-0.9777-2.10431.69381.36516.2847-0.2583-0.3894-0.60540.1327-0.24860.03040.2746-0.33420.33161.2794-0.49710.16480.9572-0.02820.7486-70.290885.635636.7742
199.59542.1076-0.03772.0196-1.74050.2971-0.0847-0.3284-0.86480.77330.17580.81322.178-1.3219-0.14691.6605-0.49770.21340.92360.08110.9488-70.276377.210539.9931
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 18:50)
2X-RAY DIFFRACTION2chain 'A' and (resseq 51:130)
3X-RAY DIFFRACTION3chain 'A' and (resseq 131:288)
4X-RAY DIFFRACTION4chain 'A' and (resseq 289:317)
5X-RAY DIFFRACTION5chain 'A' and (resseq 318:351)
6X-RAY DIFFRACTION6chain 'A' and (resseq 352:405)
7X-RAY DIFFRACTION7chain 'A' and (resseq 406:432)
8X-RAY DIFFRACTION8chain 'H' and (resseq 1:120)
9X-RAY DIFFRACTION9chain 'H' and (resseq 121:152)
10X-RAY DIFFRACTION10chain 'H' and (resseq 153:168)
11X-RAY DIFFRACTION11chain 'H' and (resseq 169:190)
12X-RAY DIFFRACTION12chain 'H' and (resseq 191:220)
13X-RAY DIFFRACTION13chain 'L' and (resseq 21:51)
14X-RAY DIFFRACTION14chain 'L' and (resseq 52:67)
15X-RAY DIFFRACTION15chain 'L' and (resseq 68:118)
16X-RAY DIFFRACTION16chain 'L' and (resseq 119:155)
17X-RAY DIFFRACTION17chain 'L' and (resseq 156:181)
18X-RAY DIFFRACTION18chain 'L' and (resseq 182:210)
19X-RAY DIFFRACTION19chain 'L' and (resseq 211:233)

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