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- PDB-3o45: Crystal Structure of 101F Fab Bound to 17-mer Peptide Epitope -

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Basic information

Entry
Database: PDB / ID: 3o45
TitleCrystal Structure of 101F Fab Bound to 17-mer Peptide Epitope
Components
  • Fusion glycoprotein F1
  • Mouse monoclonal antibody 101F 101F Fab heavy chain
  • Mouse monoclonal antibody 101F 101F Fab light chain
KeywordsIMMUNE SYSTEM/VIRAL PROTEIN / immunoglobulin / IMMUNE SYSTEM-VIRAL PROTEIN complex
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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.872 Å
AuthorsMcLellan, J.S. / Chen, M. / Chang, J.S. / Yang, Y. / Kim, A. / Graham, B.S. / Kwong, P.D.
CitationJournal: J.Virol. / Year: 2010
Title: Structure of a Major Antigenic Site on the Respiratory Syncytial Virus Fusion Glycoprotein in Complex with Neutralizing Antibody 101F.
Authors: McLellan, J.S. / Chen, M. / Chang, J.S. / Yang, Y. / Kim, A. / Graham, B.S. / Kwong, P.D.
History
DepositionJul 26, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
L: Mouse monoclonal antibody 101F 101F Fab light chain
H: Mouse monoclonal antibody 101F 101F Fab heavy chain
A: Mouse monoclonal antibody 101F 101F Fab heavy chain
B: Mouse monoclonal antibody 101F 101F Fab light chain
P: Fusion glycoprotein F1
C: Fusion glycoprotein F1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,85513
Polymers99,1836
Non-polymers6727
Water50428
1
L: Mouse monoclonal antibody 101F 101F Fab light chain
H: Mouse monoclonal antibody 101F 101F Fab heavy chain
P: Fusion glycoprotein F1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9767
Polymers49,5913
Non-polymers3844
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Mouse monoclonal antibody 101F 101F Fab heavy chain
B: Mouse monoclonal antibody 101F 101F Fab light chain
C: Fusion glycoprotein F1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8796
Polymers49,5913
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.537, 92.966, 140.918
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 Mouse monoclonal antibody 101F 101F Fab light chain


Mass: 24064.551 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#2: Antibody Mouse monoclonal antibody 101F 101F Fab heavy chain


Mass: 23704.695 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#3: Protein/peptide Fusion glycoprotein F1 / Protein F


Mass: 1822.034 Da / Num. of mol.: 2 / Fragment: UNP residues 422-438 / Source method: obtained synthetically / Details: synthetic peptide / References: UniProt: P03420
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 2.63 Å3/Da / Density % sol: 53.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 20.5% (w/v) PEG 4000, 0.2 M lithium sulfate monohydrate, 0.1 M Tris-HCl pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 18, 2010
RadiationMonochromator: Si 220. Rosenbaum-Rock double-crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.87→50 Å / Num. all: 24012 / Num. obs: 24012 / % possible obs: 98.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.87→3 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.688 / Mean I/σ(I) obs: 1.8 / % possible all: 92

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Processing

Software
NameVersionClassification
SERGUIdata collection
PHASERphasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3O41

3o41


Resolution: 2.872→25.543 Å / SU ML: 0.31 / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.254 1228 5.13 %RANDOM
Rwork0.1999 ---
obs0.2026 23958 97.95 %-
all-23958 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 0.001 Å2 / ksol: 0.316 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.7007 Å2-0 Å20 Å2
2---6.5038 Å20 Å2
3---3.4449 Å2
Refinement stepCycle: LAST / Resolution: 2.872→25.543 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6890 0 35 28 6953
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027102
X-RAY DIFFRACTIONf_angle_d0.5589678
X-RAY DIFFRACTIONf_dihedral_angle_d12.2182478
X-RAY DIFFRACTIONf_chiral_restr0.0361088
X-RAY DIFFRACTIONf_plane_restr0.0031228
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8723-2.98710.35811280.27622135X-RAY DIFFRACTION85
2.9871-3.12280.31831340.26172470X-RAY DIFFRACTION98
3.1228-3.28720.30511300.23352534X-RAY DIFFRACTION100
3.2872-3.49260.26421360.21112545X-RAY DIFFRACTION100
3.4926-3.76150.22941280.182560X-RAY DIFFRACTION100
3.7615-4.13860.21871440.1772562X-RAY DIFFRACTION100
4.1386-4.73420.20551440.14812587X-RAY DIFFRACTION100
4.7342-5.95210.21121430.16122603X-RAY DIFFRACTION100
5.9521-25.54380.25471410.20772734X-RAY DIFFRACTION100
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)
10.57770.08940.08720.1289-0.00970.0774-0.0583-0.0109-0.33320.04860.07640.2150.02120.0056-0.03440.0831-0.03640.02230.04220.03860.3184-26.951-9.7209-5.8501
20.3980.15970.24280.520.03330.2334-0.11850.194-0.0729-0.0990.0106-0.05740.02890.0892-0.06720.1424-0.10010.02140.1603-0.11470.1062-53.23120.695-30.7287
31.2644-0.10880.46450.33920.00890.28080.1097-0.0649-0.4871-0.09080.0551-0.06640.0685-0.0273-0.13580.08910.01160.01410.03920.00640.2331-65.0602-11.62369.1742
41.19760.17490.06511.0672-0.70780.60240.086-0.7319-0.14450.4215-0.2007-0.127-0.3307-0.15980.09090.1937-0.0609-0.07110.48260.07480.04-38.5676-0.96533.508
50.33630.10940.17090.55720.08740.0948-0.05590.0656-0.0085-0.11180.02640.04450.00260.0895-0.00360.0304-0.01160.03690.04350.02250.0676-20.464411.785-8.4633
60.96490.27420.18240.32540.1340.2172-0.00220.1968-0.0642-0.093-0.08060.08630.0065-0.09570.11520.1071-0.03240.03950.1508-0.1030.1177-51.080111.4373-19.9393
70.3911-0.0001-0.29580.292-0.01410.2608-0.03280.0081-0.01180.04740.1057-0.00490.0307-0.07420.02720.0390.00230.04550.078-0.01010.0873-69.461210.51169.5889
81.35010.6897-1.00951.3112-0.41911.0362-0.0925-0.3119-0.19510.1822-0.2262-0.23750.01290.1667-0.20850.0119-0.0515-0.05660.1117-0.0593-0.0434-38.93048.288121.2952
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain L and resid 1:113
2X-RAY DIFFRACTION2chain L and resid 114:218
3X-RAY DIFFRACTION3chain B and resid 1:113
4X-RAY DIFFRACTION4chain B and resid 114:218
5X-RAY DIFFRACTION5chain H and resid 1:116
6X-RAY DIFFRACTION6chain H and resid 117:218
7X-RAY DIFFRACTION7chain A and resid 1:116
8X-RAY DIFFRACTION8chain A and resid 117:218

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