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- PDB-8tw3: hMPV fusion protein complexed with single domain antibodies sdHMP... -

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Basic information

Entry
Database: PDB / ID: 8tw3
TitlehMPV fusion protein complexed with single domain antibodies sdHMPV16 and sdHMPV12
Components
  • Fusion glycoprotein
  • Single domain antibody sdHMPV12
  • Single domain antibody sdHMPV16
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / metapneumovirus / fusion protein / VIRAL PROTEIN / VIRAL PROTEIN-Immune System complex
Function / homologyPrecursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0 / fusion of virus membrane with host plasma membrane / host cell plasma membrane / virion membrane / plasma membrane / Fusion glycoprotein F0
Function and homology information
Biological speciesLama glama (llama)
Human metapneumovirus A
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsRush, S.A. / McLellan, J.S.
Funding support United States, 2items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-AC02-06CH11357 United States
Welch Foundation United States
CitationJournal: Mbio / Year: 2024
Title: A neutralizing single-domain antibody that targets the trimer interface of the human metapneumovirus fusion protein.
Authors: Ballegeer, M. / van Scherpenzeel, R.C. / Delgado, T. / Iglesias-Caballero, M. / Garcia Barreno, B. / Pandey, S. / Rush, S.A. / Kolkman, J.A. / Mas, V. / McLellan, J.S. / Saelens, X.
History
DepositionAug 19, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Single domain antibody sdHMPV12
B: Single domain antibody sdHMPV16
F: Fusion glycoprotein
X: Fusion glycoprotein
Y: Single domain antibody sdHMPV12
Z: Single domain antibody sdHMPV16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,49110
Polymers200,6066
Non-polymers8854
Water00
1
A: Single domain antibody sdHMPV12
B: Single domain antibody sdHMPV16
F: Fusion glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,7465
Polymers100,3033
Non-polymers4422
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
X: Fusion glycoprotein
Y: Single domain antibody sdHMPV12
Z: Single domain antibody sdHMPV16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,7465
Polymers100,3033
Non-polymers4422
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.260, 115.610, 158.030
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody Single domain antibody sdHMPV12


Mass: 20633.838 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Homo sapiens (human)
#2: Antibody Single domain antibody sdHMPV16


Mass: 20863.871 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Homo sapiens (human)
#3: Protein Fusion glycoprotein


Mass: 58805.473 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human metapneumovirus A / Production host: Homo sapiens (human) / References: UniProt: H6X1Z0
#4: 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.: 4 / 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

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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 / pH: 7 / Details: 0.1M HEPES and 18% PEG 12,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.9→44.97 Å / Num. obs: 32688 / % possible obs: 98.6 % / Redundancy: 5.6 % / CC1/2: 0.962 / Rmerge(I) obs: 0.214 / Rpim(I) all: 0.099 / Rrim(I) all: 0.237 / Χ2: 1.04 / Net I/σ(I): 7 / Num. measured all: 181517
Reflection shellResolution: 2.9→3.06 Å / % possible obs: 99.3 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.862 / Num. measured all: 27228 / Num. unique obs: 4780 / CC1/2: 0.638 / Rpim(I) all: 0.393 / Rrim(I) all: 0.951 / Χ2: 0.95 / Net I/σ(I) obs: 2.4

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→44.97 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2324 1541 4.72 %
Rwork0.1908 --
obs0.1927 32631 97.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→44.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9519 0 56 0 9575
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003
X-RAY DIFFRACTIONf_angle_d0.501
X-RAY DIFFRACTIONf_dihedral_angle_d11.8433556
X-RAY DIFFRACTIONf_chiral_restr0.0421521
X-RAY DIFFRACTIONf_plane_restr0.0031696
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.990.31571330.26192818X-RAY DIFFRACTION99
2.99-3.10.31041450.24492827X-RAY DIFFRACTION99
3.1-3.220.27261400.24442809X-RAY DIFFRACTION99
3.22-3.370.26441240.22412842X-RAY DIFFRACTION99
3.37-3.550.28221470.2132771X-RAY DIFFRACTION97
3.55-3.770.27621500.20032806X-RAY DIFFRACTION98
3.77-4.060.22721480.18712838X-RAY DIFFRACTION99
4.06-4.470.18291260.15442848X-RAY DIFFRACTION99
4.47-5.120.16651390.14232822X-RAY DIFFRACTION97
5.12-6.440.231560.17962848X-RAY DIFFRACTION97
6.45-44.970.19061330.17242861X-RAY DIFFRACTION93

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