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- PDB-3ixt: Crystal Structure of Motavizumab Fab Bound to Peptide Epitope -

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Basic information

Entry
Database: PDB / ID: 3ixt
TitleCrystal Structure of Motavizumab Fab Bound to Peptide Epitope
Components
  • Fusion glycoprotein F1
  • Motavizumab Fab heavy chain
  • Motavizumab Fab light chain
KeywordsIMMUNE SYSTEM / Fab / RSV / Synagis / Motavizumab / monoclonal / complex / Cell membrane / Cleavage on pair of basic residues / Disulfide bond / Envelope protein / Fusion protein / Glycoprotein / Lipoprotein / Membrane / Palmitate / Transmembrane / Virion
Function / homology
Function and homology information


positive regulation of syncytium formation by virus / Translation of respiratory syncytial virus mRNAs / RSV-host interactions / Maturation of hRSV A proteins / Assembly and release of respiratory syncytial virus (RSV) virions / host cell Golgi membrane / Respiratory syncytial virus (RSV) attachment and entry / entry receptor-mediated virion attachment to host cell / symbiont entry into host cell / fusion of virus membrane with host plasma membrane ...positive regulation of syncytium formation by virus / Translation of respiratory syncytial virus mRNAs / RSV-host interactions / Maturation of hRSV A proteins / Assembly and release of respiratory syncytial virus (RSV) virions / host cell Golgi membrane / Respiratory syncytial virus (RSV) attachment and entry / 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 / identical protein binding / plasma membrane
Similarity search - Function
Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Fusion glycoprotein F0
Similarity search - Component
Biological speciesMus musculus (house mouse)
Human respiratory syncytial virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsMcLellan, J.S. / Chen, M. / Kim, A. / Yang, Y. / Graham, B.S. / Kwong, P.D.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2010
Title: Structural basis of respiratory syncytial virus neutralization by motavizumab.
Authors: McLellan, J.S. / Chen, M. / Kim, A. / Yang, Y. / Graham, B.S. / Kwong, P.D.
History
DepositionSep 4, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: Motavizumab Fab light chain
H: Motavizumab Fab heavy chain
P: Fusion glycoprotein F1
B: Motavizumab Fab light chain
A: Motavizumab Fab heavy chain
C: Fusion glycoprotein F1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,5759
Polymers100,3896
Non-polymers1863
Water2,702150
1
L: Motavizumab Fab light chain
H: Motavizumab Fab heavy chain
P: Fusion glycoprotein F1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2564
Polymers50,1943
Non-polymers621
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Motavizumab Fab light chain
A: Motavizumab Fab heavy chain
C: Fusion glycoprotein F1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3185
Polymers50,1943
Non-polymers1242
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.752, 90.752, 232.057
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-220-

HOH

21A-242-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain L and (resseq 1:209 )
211chain B and (resseq 1:209 )
112chain H and (resseq 1:128 or resseq 137:215 )
212chain A and (resseq 1:128 or resseq 137:215 )
113chain P and (resseq 4:27 )
213chain C and (resseq 4:27 )

NCS ensembles :
ID
1
2
3

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Components

#1: Antibody Motavizumab Fab light chain


Mass: 23150.730 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: humanized-mouse antibody / Cell line (production host): 293F cells / Production host: homo sapiens (human)
#2: Antibody Motavizumab Fab heavy chain


Mass: 24284.465 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: humanized-mouse antibody / Cell line (production host): 293F cells / Production host: homo sapiens (human)
#3: Protein/peptide Fusion glycoprotein F1 / Fusion glycoprotein F0 / Protein F


Mass: 2759.143 Da / Num. of mol.: 2 / Fragment: sequence database residues 254-277 / Source method: isolated from a natural source / Source: (natural) Human respiratory syncytial virus / Strain: A2 / References: UniProt: P03420
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H2O

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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: 2.38 Å3/Da / Density % sol: 48.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 17.5% PEG 8000, 0.2 M zinc acetate, 0.1 M cacodylate pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.82656 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 4, 2009
RadiationMonochromator: Si 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.82656 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. all: 24653 / Num. obs: 23510 / % possible obs: 93.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.75→2.85 Å / % possible all: 88.3

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2HWZ

2hwz


Resolution: 2.75→33.256 Å / SU ML: 2.86 / σ(F): 0.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.274 1149 4.89 %random
Rwork0.2132 ---
obs0.2162 23502 89.66 %-
all-26212 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.71 Å2 / ksol: 0.329 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.2235 Å2-0 Å2-0 Å2
2---0.2235 Å2-0 Å2
3----0.6855 Å2
Refinement stepCycle: LAST / Resolution: 2.75→33.256 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6848 0 12 150 7010
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047025
X-RAY DIFFRACTIONf_angle_d0.7429545
X-RAY DIFFRACTIONf_dihedral_angle_d14.1642486
X-RAY DIFFRACTIONf_chiral_restr0.0541095
X-RAY DIFFRACTIONf_plane_restr0.0041208
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11L1607X-RAY DIFFRACTIONPOSITIONAL
12B1607X-RAY DIFFRACTIONPOSITIONAL0.01
21H1620X-RAY DIFFRACTIONPOSITIONAL
22A1620X-RAY DIFFRACTIONPOSITIONAL0.01
31P188X-RAY DIFFRACTIONPOSITIONAL
32C188X-RAY DIFFRACTIONPOSITIONAL0.142
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7457-2.87060.40611240.28832274X-RAY DIFFRACTION75
2.8706-3.02190.27971270.2522626X-RAY DIFFRACTION86
3.0219-3.2110.29761460.22592766X-RAY DIFFRACTION90
3.211-3.45870.31851370.232820X-RAY DIFFRACTION92
3.4587-3.80640.27151490.20352911X-RAY DIFFRACTION94
3.8064-4.35610.23431260.18062957X-RAY DIFFRACTION94
4.3561-5.48420.21221650.17232940X-RAY DIFFRACTION94
5.4842-33.2580.29481750.22523059X-RAY DIFFRACTION92
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)
11.41511.4149-0.41452.20451.68551.4865-0.04520.13240.1106-0.2761-0.04150.10610.0649-0.10030.05660.2928-0.1287-0.02680.26530.02730.2036-23.4708-0.9255-9.066
20.09950.1807-0.43111.0317-0.44633.1220.080.12520.1228-0.08120.08840.2233-0.4607-0.2987-0.19230.1992-0.08050.05460.20560.03410.2294-43.0189-16.210818.3653
3-0.06330.1309-0.17131.9614-0.26011.670.0006-0.1507-0.26860.3249-0.1834-0.49360.06760.29810.35930.1836-0.1073-0.0490.21340.05020.3572-12.974410.19877.074
40.72640.47670.72761.22140.03040.78170.13230.0874-0.1415-0.466-0.0411-0.0896-0.26420.2727-0.1460.3298-0.06950.06470.15720.04710.3779-27.0619-12.248922.5495
50.84080.79670.67761.917-0.30620.8572-0.23120.5355-0.0951-0.34020.0012-0.24640.2279-0.10640.13930.4955-0.2927-0.0170.49560.07130.1943-45.09923.2143-9.3561
61.0756-0.00360.84811.2942-1.13182.9405-0.0461-0.18140.19540.2233-0.1814-0.20090.04650.35770.24850.3855-0.0918-0.05020.41820.01260.2269-26.083437.689818.7756
70.48570.94010.68322.03960.42761.8537-0.0272-0.1227-0.03550.2127-0.03620.0670.1485-0.50890.01140.3375-0.1943-0.10980.39570.10490.3095-55.729111.62596.3139
81.4273-0.9699-0.01930.902-1.70353.73330.1404-0.02670.33980.06030.1040.1135-0.1965-0.4231-0.20440.3509-0.0465-0.05650.2704-0.00370.3397-42.069133.488622.6963
91.1412-1.0066-0.37182.67520.68914.12230.0831-0.10260.5171-0.2798-0.5869-1.5353-0.88150.67390.36860.7614-0.33160.25240.52660.09780.5419-1.701914.5149-12.1694
100.4483-1.4767-3.5778-0.4464-0.76350.7687-0.90760.83220.10630.2797-0.11370.63290.6518-0.49860.40411.016-0.4602-0.18970.71620.01150.3704-66.94267.959-13.2454
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain L and resid 1:106L1 - 106
2X-RAY DIFFRACTION2chain L and resid 107:213L107 - 213
3X-RAY DIFFRACTION3chain H and resid 1:113H1 - 113
4X-RAY DIFFRACTION4chain H and resid 114:218H114 - 218
5X-RAY DIFFRACTION5chain B and resid 1:106B1 - 106
6X-RAY DIFFRACTION6chain B and resid 107:213B107 - 213
7X-RAY DIFFRACTION7chain A and resid 1:113A1 - 113
8X-RAY DIFFRACTION8chain A and resid 114:218A114 - 218
9X-RAY DIFFRACTION9chain PP253 - 278
10X-RAY DIFFRACTION10chain CC253 - 278

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