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- PDB-6uvo: Structure of antibody 3G12 bound to the central conserved domain ... -

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Basic information

Entry
Database: PDB / ID: 6uvo
TitleStructure of antibody 3G12 bound to the central conserved domain of RSV G
Components
  • 3G12 Fab Heavy chain
  • 3G12 Fab light chain
  • Major surface glycoprotein G
KeywordsVIRAL PROTEIN / IMMUNE SYSTEM / RSV / glycoprotein / G glycoprotein / viral attachment protein / antibody
Function / homology
Function and homology information


Assembly and release of respiratory syncytial virus (RSV) virions / Translation of respiratory syncytial virus mRNAs / Respiratory syncytial virus (RSV) attachment and entry / adhesion receptor-mediated virion attachment to host cell / RSV-host interactions / Maturation of hRSV A proteins / symbiont entry into host cell / virus-mediated perturbation of host defense response / host cell plasma membrane / virion membrane ...Assembly and release of respiratory syncytial virus (RSV) virions / Translation of respiratory syncytial virus mRNAs / Respiratory syncytial virus (RSV) attachment and entry / adhesion receptor-mediated virion attachment to host cell / RSV-host interactions / Maturation of hRSV A proteins / 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: 2.9 Å
AuthorsFedechkin, S.O. / George, N.L. / Nunez Castrejon, A.M. / Dillen, J. / Kauvar, L.M. / DuBois, R.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R21AI130605 United States
CitationJournal: J.Virol. / Year: 2020
Title: Conformational Flexibility in Respiratory Syncytial Virus G Neutralizing Epitopes.
Authors: Fedechkin, S.O. / George, N.L. / Nunez Castrejon, A.M. / Dillen, J.R. / Kauvar, L.M. / DuBois, R.M.
History
DepositionNov 3, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Mar 11, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.title / _citation.year
Revision 1.3Oct 11, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: 3G12 Fab light chain
H: 3G12 Fab Heavy chain
D: Major surface glycoprotein G


Theoretical massNumber of molelcules
Total (without water)53,7933
Polymers53,7933
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5900 Å2
ΔGint-35 kcal/mol
Surface area20510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.330, 139.330, 94.770
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Antibody 3G12 Fab light chain


Mass: 23218.771 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody 3G12 Fab Heavy chain


Mass: 24838.816 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Protein/peptide Major surface glycoprotein G / Attachment glycoprotein G / Membrane-bound glycoprotein / mG


Mass: 5735.633 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human respiratory syncytial virus A (strain A2)
Strain: A2 / Production host: Escherichia coli (E. coli) / References: UniProt: P03423

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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: 5.19 Å3/Da / Density % sol: 76.29 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion / pH: 4.4
Details: 1.8M Ammonium Sulfate, 100mM sodium acetate trihydrate pH4.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11503 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 24, 2018 / Details: Pilatus3 S, 25Hz, S/N 60-0134
RadiationMonochromator: Si(111) Khozu / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11503 Å / Relative weight: 1
ReflectionResolution: 2.9→74.531 Å / Num. obs: 23682 / % possible obs: 99.5 % / Redundancy: 3.9 % / Biso Wilson estimate: 66.24 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.062 / Rrim(I) all: 0.126 / Net I/σ(I): 9.4
Reflection shell

Diffraction-ID: 1 / Redundancy: 3.8 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.9-3.080.7321447537630.6010.4190.8471.999.5
8.7-74.530.03735619340.9970.0220.04321.198.4

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
Aimless0.5.27data scaling
PDB_EXTRACT3.24data extraction
iMOSFLMdata reduction
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5K59

5k59


Resolution: 2.9→74.53 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 20.56
RfactorNum. reflection% reflection
Rfree0.2088 1993 8.42 %
Rwork0.193 --
obs0.1943 23665 99.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 190.21 Å2 / Biso mean: 63.3008 Å2 / Biso min: 27.71 Å2
Refinement stepCycle: final / Resolution: 2.9→74.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3595 0 0 0 3595
Num. residues----471
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0193693
X-RAY DIFFRACTIONf_angle_d2.0675040
X-RAY DIFFRACTIONf_chiral_restr0.243566
X-RAY DIFFRACTIONf_plane_restr0.008643
X-RAY DIFFRACTIONf_dihedral_angle_d24.0511324
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.9002-2.97270.31091390.2958153399
2.9727-3.05310.29511390.3046151299
3.0531-3.14290.30511450.28221533100
3.1429-3.24440.3181420.24921540100
3.2444-3.36030.24361430.2389153799
3.3603-3.49490.25761430.2181153799
3.4949-3.65390.22661430.2027154499
3.6539-3.84660.24061420.20621528100
3.8466-4.08760.18381430.1749154899
4.0876-4.40310.16771400.14471548100
4.4031-4.84620.15791420.1449154999
4.8462-5.54720.18131450.15211578100
5.5472-6.98810.21851450.2062157399
6.9881-74.530.16371420.188161297
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)
10.6408-0.3531-0.03365.0262-1.57571.6970.03540.0268-0.07260.3340.0590.5314-0.0995-0.1187-0.08160.3407-0.0571-0.0170.3948-0.01210.3468-63.199740.421246.3516
20.59090.22330.07223.5267-1.1361.13150.069-0.0693-0.1112-0.0438-0.1129-0.1460.14770.19450.06470.31280.0087-0.0360.4352-0.01870.3531-50.016129.357640.0192
36.51065.0188-2.05355.054-0.69114.01440.1297-0.3054-0.01010.3036-0.33570.14120.7740.62780.19650.66170.0211-0.10040.4010.07730.5704-56.8687-0.989855.4021
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'L' and (resid 1 through 212 )L1 - 212
2X-RAY DIFFRACTION2chain 'H' and (resid 2 through 229 )H2 - 229
3X-RAY DIFFRACTION3chain 'D' and (resid 160 through 189 )D160 - 189

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