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- PDB-6w16: Crystal structure of a human metapneumovirus monomeric fusion pro... -

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Basic information

Entry
Database: PDB / ID: 6w16
TitleCrystal structure of a human metapneumovirus monomeric fusion protein complexed with 458 Fab
Components
  • 458 Fab heavy chain
  • 458 Fab light chain
  • Fusion glycoprotein F0,Envelope glycoprotein fusion
KeywordsIMMUNE SYSTEM / antibody / F protein
Function / homology
Function and homology information


fusion of virus membrane with host plasma membrane / viral envelope / symbiont entry into host cell / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0 / Fibritin C-terminal / Fibritin C-terminal region / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Envelope glycoprotein / Fusion glycoprotein F0
Similarity search - Component
Biological speciesHuman metapneumovirus
Human immunodeficiency virus 1
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsHuang, J. / Mousa, J.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI14386 United States
CitationJournal: Plos Pathog. / Year: 2020
Title: Antibody recognition of the Pneumovirus fusion protein trimer interface.
Authors: Huang, J. / Diaz, D. / Mousa, J.J.
History
DepositionMar 3, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2020Provider: repository / Type: Initial release
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 / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _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.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_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 10, 2021Group: Database references / Structure summary / Category: chem_comp / citation / citation_author
Item: _chem_comp.pdbx_synonyms / _citation.country ..._chem_comp.pdbx_synonyms / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.3Nov 6, 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

Downloads & links

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Assembly

Deposited unit
F: Fusion glycoprotein F0,Envelope glycoprotein fusion
H: 458 Fab heavy chain
L: 458 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,1345
Polymers106,0023
Non-polymers1,1322
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7100 Å2
ΔGint-13 kcal/mol
Surface area37940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.489, 128.489, 188.352
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Space group name HallP65
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: -x,-y,z+1/2

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Components

#1: Protein Fusion glycoprotein F0,Envelope glycoprotein fusion


Mass: 59099.973 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human metapneumovirus, (gene. exp.) Human immunodeficiency virus 1
Production host: Homo sapiens (human) / References: UniProt: Q6W8S4, UniProt: M1E1E4
#2: Antibody 458 Fab heavy chain


Mass: 23316.221 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody 458 Fab light chain


Mass: 23586.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#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.: 1 / Source method: obtained synthetically
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
#5: 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: 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
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: 4.23 Å3/Da / Density % sol: 70.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.5 M Ammonium sulfate, 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 1.0 M Lithium sulfate monohydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Oct 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→47.9 Å / Num. obs: 31997 / % possible obs: 100 % / Redundancy: 21 % / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1407 / Rpim(I) all: 0.03155 / Rrim(I) all: 0.1443 / Net I/σ(I): 17.62
Reflection shellResolution: 3.1→3.27 Å / Redundancy: 20.9 % / Num. unique obs: 4679 / CC1/2: 0.621 / CC star: 0.875 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WB0

5wb0


Resolution: 3.1→41.05 Å / SU ML: 0.4638 / Cross valid method: FREE R-VALUE / Phase error: 26.639
RfactorNum. reflection% reflection
Rfree0.2339 3241 10.15 %
Rwork0.1897 --
obs0.1934 31943 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.1→41.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6190 0 75 0 6265
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0116376
X-RAY DIFFRACTIONf_angle_d1.25698652
X-RAY DIFFRACTIONf_chiral_restr0.06831021
X-RAY DIFFRACTIONf_plane_restr0.00771100
X-RAY DIFFRACTIONf_dihedral_angle_d16.58862325
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.150.38051470.33131269X-RAY DIFFRACTION100
3.15-3.20.35251550.30911199X-RAY DIFFRACTION100
3.2-3.250.37691790.29371216X-RAY DIFFRACTION100
3.25-3.30.34941630.29171229X-RAY DIFFRACTION100
3.3-3.360.3321390.2661234X-RAY DIFFRACTION100
3.36-3.430.30931370.25461262X-RAY DIFFRACTION100
3.43-3.50.33181350.24121228X-RAY DIFFRACTION100
3.5-3.570.33281550.24641250X-RAY DIFFRACTION100
3.57-3.660.27361320.23271243X-RAY DIFFRACTION100
3.66-3.750.29611240.23111252X-RAY DIFFRACTION99.93
3.75-3.850.2771270.21681258X-RAY DIFFRACTION100
3.85-3.960.27461350.21341253X-RAY DIFFRACTION100
3.96-4.090.25051640.20511226X-RAY DIFFRACTION100
4.09-4.240.22761070.17981274X-RAY DIFFRACTION100
4.24-4.410.21721430.15521244X-RAY DIFFRACTION100
4.41-4.610.20561220.15211269X-RAY DIFFRACTION100
4.61-4.850.20341430.15611250X-RAY DIFFRACTION100
4.85-5.150.1791430.15541249X-RAY DIFFRACTION100
5.15-5.550.23311240.17211264X-RAY DIFFRACTION100
5.55-6.110.23871210.17551270X-RAY DIFFRACTION100
6.11-6.980.21261560.19151223X-RAY DIFFRACTION100
6.99-8.780.18631480.16051264X-RAY DIFFRACTION100
8.79-41.050.18281420.17191264X-RAY DIFFRACTION99.22

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