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- PDB-5wn9: Structure of antibody 2D10 bound to the central conserved region ... -

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Basic information

Entry
Database: PDB / ID: 5wn9
TitleStructure of antibody 2D10 bound to the central conserved region of RSV G
Components
  • Major surface glycoprotein G
  • scFv 2D10
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / RSV / glycoprotein / G glycoprotein / viral protein / viral attachment protein / antibody / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


Translation of respiratory syncytial virus mRNAs / adhesion receptor-mediated virion attachment to host cell / RSV-host interactions / Assembly and release of respiratory syncytial virus (RSV) virions / Maturation of hRSV A proteins / Respiratory syncytial virus (RSV) attachment and entry / symbiont entry into host cell / virus-mediated perturbation of host defense response / host cell plasma membrane / virion membrane ...Translation of respiratory syncytial virus mRNAs / adhesion receptor-mediated virion attachment to host cell / RSV-host interactions / Assembly and release of respiratory syncytial virus (RSV) virions / Maturation of hRSV A proteins / Respiratory syncytial virus (RSV) attachment and entry / symbiont entry into host cell / virus-mediated perturbation of host defense response / host cell plasma membrane / virion membrane / extracellular region / plasma membrane
Similarity search - Function
Major surface glycoprotein G / Pneumovirus attachment glycoprotein G / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Major surface glycoprotein G
Similarity search - Component
Biological speciesHomo sapiens (human)
Human respiratory syncytial virus A
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.551 Å
AuthorsFedechkin, S.O. / George, N.L. / Wolff, J.T. / Kauvar, L.M. / DuBois, R.M.
CitationJournal: Sci Immunol / Year: 2018
Title: Structures of respiratory syncytial virus G antigen bound to broadly neutralizing antibodies.
Authors: Fedechkin, S.O. / George, N.L. / Wolff, J.T. / Kauvar, L.M. / DuBois, R.M.
History
DepositionJul 31, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 4, 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 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: scFv 2D10
A: Major surface glycoprotein G


Theoretical massNumber of molelcules
Total (without water)30,4902
Polymers30,4902
Non-polymers00
Water2,000111
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, 2D10 scFv co-elutes with RSV G 169-198 peptide
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area990 Å2
ΔGint-5 kcal/mol
Surface area11730 Å2
Unit cell
Length a, b, c (Å)44.843, 56.387, 126.148
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody scFv 2D10


Mass: 27218.131 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Drosophila melanogaster (fruit fly)
#2: Protein/peptide Major surface glycoprotein G / Attachment glycoprotein G / Membrane-bound glycoprotein / mG


Mass: 3271.921 Da / Num. of mol.: 1
Fragment: Central conserved region of RSV G, UNP residues 168-196
Source method: obtained synthetically / Details: synthetic peptide
Source: (synth.) Human respiratory syncytial virus A (strain A2)
References: UniProt: P03423
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O
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: 2.62 Å3/Da / Density % sol: 52.97 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 25% PEG4000, 0.17M Ammonium acetate, 0.085 sodium citrate pH 5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 11, 2016
Details: iger 1M with max frame rate of 133 Hz: Count rate 2MHz/pixel. Mini-beam 5 or 10 micron beam
RadiationMonochromator: Si(111) Khozu / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.55→42.253 Å / Num. obs: 47198 / % possible obs: 99.9 % / Redundancy: 9.6 % / Biso Wilson estimate: 25.1 Å2 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.023 / Rrim(I) all: 0.074 / Χ2: 1.294 / Net I/σ(I): 8.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allΧ2% possible allRrim(I) all
1.55-1.586.20.95322900.7510.3890.45699.4
1.58-1.617.20.89423350.8040.3460.46499.90.962
1.61-1.647.90.83623150.8280.3120.4761000.894
1.64-1.678.90.76423220.8820.2690.4811000.811
1.67-1.719.50.64923360.9170.2230.4981000.687
1.71-1.7510.30.50322970.9560.1650.5451000.53
1.75-1.7910.40.40323630.9720.1320.5821000.424
1.79-1.8410.20.3223170.9730.1060.6431000.338
1.84-1.89100.25423550.9820.0850.7221000.268
1.89-1.959.50.20123330.9870.0690.91999.90.212
1.95-2.029.90.1623300.9910.0541.0471000.169
2.02-2.110.50.14223490.9910.0461.1431000.149
2.1-2.210.60.12123530.9940.0391.3011000.127
2.2-2.3210.50.10323530.9950.0341.4751000.109
2.32-2.46100.09323820.9950.0311.6651000.098
2.46-2.6510.20.08123720.9960.0271.9431000.086
2.65-2.9210.90.07423760.9970.0242.3041000.078
2.92-3.3410.40.06423940.9980.0212.6391000.068
3.34-4.219.70.05424390.9980.0182.8311000.057
4.21-509.70.04725870.9990.0162.48699.80.05

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data reduction
SCALEPACKdata scaling
PDB_EXTRACT3.22data extraction
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NCJ, 5K9Q

3ncj

5k9q


Resolution: 1.551→42.253 Å / SU ML: 0.17 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 18.94 / Details: PHENIX
RfactorNum. reflection% reflection
Rfree0.1851 2000 4.25 %
Rwork0.1689 --
obs0.1696 47114 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 195.08 Å2 / Biso mean: 38.5981 Å2 / Biso min: 19.88 Å2
Refinement stepCycle: final / Resolution: 1.551→42.253 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1925 0 0 111 2036
Biso mean---37.92 -
Num. residues----257
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082002
X-RAY DIFFRACTIONf_angle_d0.9682735
X-RAY DIFFRACTIONf_chiral_restr0.06305
X-RAY DIFFRACTIONf_plane_restr0.006351
X-RAY DIFFRACTIONf_dihedral_angle_d19.0041200
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5509-1.58970.29651360.2853066320297
1.5897-1.63260.28411420.249631963338100
1.6326-1.68070.24891410.22631903331100
1.6807-1.73490.21481410.202831873328100
1.7349-1.79690.18661420.185831983340100
1.7969-1.86890.2061420.178931923334100
1.8689-1.9540.21491410.169731903331100
1.954-2.0570.1831430.16132083351100
2.057-2.18580.18411410.158432033344100
2.1858-2.35460.15961430.164732403383100
2.3546-2.59150.16671430.167832203363100
2.5915-2.96640.17641460.167332793425100
2.9664-3.7370.17481460.16133013447100
3.737-42.26840.18741530.161934443597100
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)
16.4704-6.5333-4.56058.86325.79374.9854-0.31010.2451-0.6585-0.106-0.19830.63540.0198-0.18840.5240.32680.0262-0.06380.28640.00070.1494-7.8403-9.85332.9016
21.0247-0.6536-0.31862.92591.34532.118-0.05070.05940.0376-0.05210.03420.2036-0.1023-0.05510.01080.24810.0176-0.02050.2046-0.0090.1896-6.2359-4.142511.8628
32.8436-0.80430.26436.61362.51236.95790.03270.1006-0.1473-0.42780.14760.0173-0.20480.3698-0.1710.2627-0.05150.01120.21780.01370.16012.05921.433910.021
40.31250.154-0.05661.0567-0.26570.9675-0.03320.03780.0044-0.1354-0.03670.0305-0.0701-0.01930.09630.26770.017-0.0080.2573-0.02140.2391-3.6186-8.814313.3672
52.37011.0199-0.23654.6776-0.48561.72420.0573-0.0355-0.06930.0884-0.09130.1879-0.0226-0.03010.04320.18790.0190.01320.2148-0.01880.1973-8.1892-13.773428.8866
62.05411.5026-0.14994.2327-0.48591.05130.0336-0.0681-0.08780.0251-0.01590.2943-0.0587-0.1404-0.0190.21590.0225-0.0210.2605-0.00350.2448-9.6029-13.482129.5687
72.1691-2.9448-3.18226.28613.77698.20380.01630.32690.3196-1.19970.0655-0.2839-0.90840.28560.07850.4269-0.0632-0.01140.31980.02360.32627.426811.810520.1307
88.0573-1.64010.61563.2248-5.13649.1563-0.21210.09920.4177-0.017-0.1738-0.273-0.52580.37210.09610.4256-0.05420.00010.2344-0.02030.28363.140510.879917.4445
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'H' and (resid 1 through 17 )H1 - 17
2X-RAY DIFFRACTION2chain 'H' and (resid 18 through 52 )H18 - 52
3X-RAY DIFFRACTION3chain 'H' and (resid 53 through 73 )H53 - 73
4X-RAY DIFFRACTION4chain 'H' and (resid 74 through 157 )H74 - 157
5X-RAY DIFFRACTION5chain 'H' and (resid 158 through 192 )H158 - 192
6X-RAY DIFFRACTION6chain 'H' and (resid 193 through 252 )H193 - 252
7X-RAY DIFFRACTION7chain 'A' and (resid 169 through 179 )A169 - 179
8X-RAY DIFFRACTION8chain 'A' and (resid 180 through 189 )A180 - 189

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