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- PDB-6blh: RSV G central conserved region bound to Fab CB017.5 -

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Basic information

Entry
Database: PDB / ID: 6blh
TitleRSV G central conserved region bound to Fab CB017.5
Components
  • Fab CB017.5 heavy chain
  • Fab CB017.5 light chain
  • Major surface glycoprotein G
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Antibody / RSV / Attachment / RSV G / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane / virion membrane / extracellular region / 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: 2 Å
AuthorsJones, H.G. / McLellan, J.S. / Langedijk, J.P.
CitationJournal: PLoS Pathog. / Year: 2018
Title: Structural basis for recognition of the central conserved region of RSV G by neutralizing human antibodies.
Authors: Jones, H.G. / Ritschel, T. / Pascual, G. / Brakenhoff, J.P.J. / Keogh, E. / Furmanova-Hollenstein, P. / Lanckacker, E. / Wadia, J.S. / Gilman, M.S.A. / Williamson, R.A. / Roymans, D. / van ...Authors: Jones, H.G. / Ritschel, T. / Pascual, G. / Brakenhoff, J.P.J. / Keogh, E. / Furmanova-Hollenstein, P. / Lanckacker, E. / Wadia, J.S. / Gilman, M.S.A. / Williamson, R.A. / Roymans, D. / van 't Wout, A.B. / Langedijk, J.P. / McLellan, J.S.
History
DepositionNov 10, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.0Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Polymer sequence / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_poly / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_poly.pdbx_seq_one_letter_code_can
Revision 2.1Nov 6, 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
L: Fab CB017.5 light chain
H: Fab CB017.5 heavy chain
G: Major surface glycoprotein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1794
Polymers53,1173
Non-polymers621
Water10,106561
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5460 Å2
ΔGint-27 kcal/mol
Surface area21250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.069, 189.646, 74.140
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11L-671-

HOH

21H-301-

HOH

31H-490-

HOH

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Components

#1: Antibody Fab CB017.5 light chain


Mass: 22837.125 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): FreeStyle 293F / Production host: Homo sapiens (human)
#2: Antibody Fab CB017.5 heavy chain


Mass: 25097.162 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): FreeStyle 293F / Production host: Homo sapiens (human)
#3: Protein/peptide Major surface glycoprotein G / Attachment glycoprotein G / Membrane-bound glycoprotein / mG


Mass: 5183.040 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Human respiratory syncytial virus A (strain rsb6256)
References: UniProt: P27025
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 561 / 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: 2.81 Å3/Da / Density % sol: 56.3 % / Description: Medium-sized, flat plates.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 23.7% Isopropanol, 11.85% PEG4k, 0.1M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→41.9 Å / Num. obs: 40222 / % possible obs: 98.5 % / Redundancy: 5.8 % / CC1/2: 0.988 / Net I/σ(I): 5.3
Reflection shellResolution: 2→2.05 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2939 / CC1/2: 0.901 / % possible all: 98.7

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Processing

Software
NameVersionClassification
PHENIX1.11.1refinement
MOSFLM7.2.1data reduction
Aimless0.5.17data scaling
PHASER7.0.033phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8FAB, 4HPY

8fab

4hpy


Resolution: 2→41.873 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 21.71
RfactorNum. reflection% reflectionSelection details
Rfree0.2257 1977 4.92 %random
Rwork0.187 ---
obs0.1889 40202 98.22 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→41.873 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3530 0 4 562 4096
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023630
X-RAY DIFFRACTIONf_angle_d0.5234956
X-RAY DIFFRACTIONf_dihedral_angle_d12.6742164
X-RAY DIFFRACTIONf_chiral_restr0.043559
X-RAY DIFFRACTIONf_plane_restr0.004631
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0001-2.05010.24981370.23912701X-RAY DIFFRACTION99
2.0501-2.10550.26061490.23192703X-RAY DIFFRACTION99
2.1055-2.16750.25441360.21442723X-RAY DIFFRACTION99
2.1675-2.23740.26521500.22472705X-RAY DIFFRACTION99
2.2374-2.31740.26671310.21842689X-RAY DIFFRACTION97
2.3174-2.41020.27321380.21522699X-RAY DIFFRACTION98
2.4102-2.51980.24361430.21312714X-RAY DIFFRACTION99
2.5198-2.65270.27771430.20722757X-RAY DIFFRACTION99
2.6527-2.81880.22131340.20242717X-RAY DIFFRACTION98
2.8188-3.03640.24761510.19392662X-RAY DIFFRACTION96
3.0364-3.34190.21561360.18562764X-RAY DIFFRACTION99
3.3419-3.82520.20881330.16842761X-RAY DIFFRACTION99
3.8252-4.81820.17791450.14822747X-RAY DIFFRACTION97
4.8182-41.88180.2041510.16232883X-RAY DIFFRACTION98

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