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- PDB-4zyp: Crystal Structure of Motavizumab and Quaternary-Specific RSV-Neut... -

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Basic information

Entry
Database: PDB / ID: 4zyp
TitleCrystal Structure of Motavizumab and Quaternary-Specific RSV-Neutralizing Human Antibody AM14 in Complex with Prefusion RSV F Glycoprotein
Components
  • AM14 antibody Fab heavy chain
  • AM14 antibody light chain
  • Fusion glycoprotein F0,Fibritin
  • Motavizumab antibody Fab heavy chain
  • Motavizumab antibody light chain
KeywordsIMMUNE SYSTEM / Ig domain / Fab / fusion / respiratory syncytial virus / prefusion
Function / homology
Function and homology information


positive regulation of syncytium formation by virus / host cell Golgi membrane / entry receptor-mediated virion attachment to host cell / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / viral envelope / host cell plasma membrane / virion membrane / membrane / identical protein binding
Similarity search - Function
Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0 / Fibritin C-terminal / Fibritin C-terminal region
Similarity search - Domain/homology
Fibritin / Fusion glycoprotein F0
Similarity search - Component
Biological speciesHuman respiratory syncytial virus A
Enterobacteria phage T4 (virus)
Mus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 5.5 Å
AuthorsGilman, M.S.A. / McLellan, J.S.
CitationJournal: Plos Pathog. / Year: 2015
Title: Characterization of a Prefusion-Specific Antibody That Recognizes a Quaternary, Cleavage-Dependent Epitope on the RSV Fusion Glycoprotein.
Authors: Gilman, M.S. / Moin, S.M. / Mas, V. / Chen, M. / Patel, N.K. / Kramer, K. / Zhu, Q. / Kabeche, S.C. / Kumar, A. / Palomo, C. / Beaumont, T. / Baxa, U. / Ulbrandt, N.D. / Melero, J.A. / ...Authors: Gilman, M.S. / Moin, S.M. / Mas, V. / Chen, M. / Patel, N.K. / Kramer, K. / Zhu, Q. / Kabeche, S.C. / Kumar, A. / Palomo, C. / Beaumont, T. / Baxa, U. / Ulbrandt, N.D. / Melero, J.A. / Graham, B.S. / McLellan, J.S.
History
DepositionMay 21, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fusion glycoprotein F0,Fibritin
B: Fusion glycoprotein F0,Fibritin
C: Fusion glycoprotein F0,Fibritin
J: Motavizumab antibody Fab heavy chain
L: Motavizumab antibody light chain
F: AM14 antibody Fab heavy chain
G: AM14 antibody light chain
H: AM14 antibody Fab heavy chain
I: AM14 antibody light chain
D: AM14 antibody Fab heavy chain
E: AM14 antibody light chain
K: Motavizumab antibody Fab heavy chain
M: Motavizumab antibody light chain
N: Motavizumab antibody Fab heavy chain
O: Motavizumab antibody light chain


Theoretical massNumber of molelcules
Total (without water)451,60915
Polymers451,60915
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)114.380, 210.290, 118.200
Angle α, β, γ (deg.)90.00, 100.46, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Fusion glycoprotein F0,Fibritin / Protein F


Mass: 55120.879 Da / Num. of mol.: 3 / Mutation: S155C, S190F, V207L, S290C, I379V, M447V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human respiratory syncytial virus A (strain A2), (gene. exp.) Enterobacteria phage T4 (virus)
Strain: A2 / Plasmid: p(alpha)H / Gene: wac, T4Tp161 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: P03420, UniProt: D9IEJ2
#2: Antibody Motavizumab antibody Fab heavy chain


Mass: 24284.465 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: Humanized mouse antibody / Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pVRC8400 / Cell line (production host): HEK293F / Production host: Homo sapiens (human)
#3: Antibody Motavizumab antibody light chain


Mass: 23150.730 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: Humanized mouse antibody / Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pVRC8400 / Production host: Homo sapiens (human)
#4: Antibody AM14 antibody Fab heavy chain


Mass: 24365.150 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pVRC8400 / Cell line (production host): HEK293F / Production host: Homo sapiens (human)
#5: Antibody AM14 antibody light chain


Mass: 23615.227 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pVRC8400 / Cell line (production host): HEK293F / Production host: Homo sapiens (human)

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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: 3.1 Å3/Da / Density % sol: 60.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 5.645mg/mL EndoH digested DS-Cav1 + AM14 Fab + Motavizumab Fab, 11.4% PEG8000, 1.71% MPD, 0.1M Imidazole pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 5.5→49.59 Å / Num. obs: 17434 / % possible obs: 97.5 % / Redundancy: 3 % / Biso Wilson estimate: 161.85 Å2 / CC1/2: 0.939 / Rmerge(I) obs: 0.182 / Rpim(I) all: 0.125 / Net I/σ(I): 4.8 / Num. measured all: 51879 / Scaling rejects: 33
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
5.5-6.152.90.7891.51429549310.5530.54497.6
12.3-49.5930.06713467015650.9160.04995.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Aimless0.3.11data scaling
PDB_EXTRACT3.15data extraction
Cootmodel building
PHASERphasing
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JHW, 3IXT, 4ZYK

4jhw

3ixt

4zyk


Resolution: 5.5→49.386 Å / SU ML: 0.91 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2768 857 4.93 %Random selection
Rwork0.2105 ---
obs0.2137 17391 97.11 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 5.5→49.386 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29990 0 0 0 29990
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00630647
X-RAY DIFFRACTIONf_angle_d1.34841583
X-RAY DIFFRACTIONf_dihedral_angle_d12.81211079
X-RAY DIFFRACTIONf_chiral_restr0.0514817
X-RAY DIFFRACTIONf_plane_restr0.0065279
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
5.5001-5.84420.36891500.31622736X-RAY DIFFRACTION97
5.8442-6.29460.36681540.28252741X-RAY DIFFRACTION97
6.2946-6.92650.30551300.25862757X-RAY DIFFRACTION98
6.9265-7.92520.30331430.2242774X-RAY DIFFRACTION97
7.9252-9.97140.22151440.17392769X-RAY DIFFRACTION97
9.9714-49.38780.23321360.16352757X-RAY DIFFRACTION96

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