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- PDB-6bli: RSV G peptide bound to Fab CB002.5 -

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Basic information

Entry
Database: PDB / ID: 6bli
TitleRSV G peptide bound to Fab CB002.5
Components
  • CB002.5 Fab Heavy Chain
  • CB002.5 Fab Light Chain
  • Major surface glycoprotein G
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Antibody / Viral attachment protein / 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: 2.12 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 13, 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
A: CB002.5 Fab Heavy Chain
B: CB002.5 Fab Light Chain
C: Major surface glycoprotein G
D: CB002.5 Fab Heavy Chain
E: CB002.5 Fab Light Chain
F: Major surface glycoprotein G
G: CB002.5 Fab Heavy Chain
H: CB002.5 Fab Light Chain
I: Major surface glycoprotein G
J: CB002.5 Fab Heavy Chain
K: CB002.5 Fab Light Chain
L: Major surface glycoprotein G


Theoretical massNumber of molelcules
Total (without water)213,25412
Polymers213,25412
Non-polymers00
Water33,0031832
1
A: CB002.5 Fab Heavy Chain
B: CB002.5 Fab Light Chain
C: Major surface glycoprotein G


Theoretical massNumber of molelcules
Total (without water)53,3143
Polymers53,3143
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5270 Å2
ΔGint-38 kcal/mol
Surface area20780 Å2
MethodPISA
2
D: CB002.5 Fab Heavy Chain
E: CB002.5 Fab Light Chain
F: Major surface glycoprotein G


Theoretical massNumber of molelcules
Total (without water)53,3143
Polymers53,3143
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5350 Å2
ΔGint-36 kcal/mol
Surface area21010 Å2
MethodPISA
3
G: CB002.5 Fab Heavy Chain
H: CB002.5 Fab Light Chain
I: Major surface glycoprotein G


Theoretical massNumber of molelcules
Total (without water)53,3143
Polymers53,3143
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5390 Å2
ΔGint-39 kcal/mol
Surface area21070 Å2
MethodPISA
4
J: CB002.5 Fab Heavy Chain
K: CB002.5 Fab Light Chain
L: Major surface glycoprotein G


Theoretical massNumber of molelcules
Total (without water)53,3143
Polymers53,3143
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5280 Å2
ΔGint-40 kcal/mol
Surface area20530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.760, 85.230, 214.300
Angle α, β, γ (deg.)90.00, 95.03, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-537-

HOH

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Components

#1: Antibody
CB002.5 Fab Heavy Chain


Mass: 24605.484 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): FreeStyle 293-F Cells / Production host: Homo sapiens (human)
#2: Antibody
CB002.5 Fab Light Chain


Mass: 23525.039 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): FreeStyle 293-F Cells / 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.: 4 / Source method: obtained synthetically
Details: A peptide encompassing the RSV G central conserved region which includes two disulfide bonds which form a cysteine noose.
Source: (synth.) Human respiratory syncytial virus A (strain rsb6256)
References: UniProt: P27025
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1832 / 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: 2.43 Å3/Da / Density % sol: 49.31 %
Description: Large, flat plates (some crystals looked more like wide rods, while others were clearly plates).
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 14.9% (w/v) PEG 3,350 and 0.1 M succinic acid.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.12→43.13 Å / Num. obs: 114818 / % possible obs: 99.2 % / Redundancy: 2.9 % / CC1/2: 0.988 / Rmerge(I) obs: 0.174 / Net I/σ(I): 4
Reflection shellResolution: 2.12→2.16 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.487 / Num. unique obs: 5719 / CC1/2: 0.901 / % possible all: 99.5

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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: 4NPY, 5IT2

4npy

5it2


Resolution: 2.12→43.128 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.55
RfactorNum. reflection% reflectionSelection details
Rfree0.218 5573 4.86 %random
Rwork0.1691 ---
obs0.1714 114768 99.05 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.12→43.128 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14178 0 0 1837 16015
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00814564
X-RAY DIFFRACTIONf_angle_d0.97419859
X-RAY DIFFRACTIONf_dihedral_angle_d7.2428613
X-RAY DIFFRACTIONf_chiral_restr0.0572231
X-RAY DIFFRACTIONf_plane_restr0.0062518
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.12-2.14410.29821820.23223669X-RAY DIFFRACTION99
2.1441-2.16930.29091850.21713597X-RAY DIFFRACTION100
2.1693-2.19580.27911820.21243625X-RAY DIFFRACTION99
2.1958-2.22360.28651950.21143696X-RAY DIFFRACTION100
2.2236-2.25280.27531730.20783581X-RAY DIFFRACTION99
2.2528-2.28370.26211760.21023682X-RAY DIFFRACTION99
2.2837-2.31630.24942040.20053556X-RAY DIFFRACTION99
2.3163-2.35090.28861890.19783630X-RAY DIFFRACTION99
2.3509-2.38760.25881990.19393576X-RAY DIFFRACTION99
2.3876-2.42680.26531950.19143632X-RAY DIFFRACTION99
2.4268-2.46860.24292000.18423594X-RAY DIFFRACTION99
2.4686-2.51350.23041770.18983644X-RAY DIFFRACTION99
2.5135-2.56180.24911740.18673613X-RAY DIFFRACTION99
2.5618-2.61410.24261780.18943610X-RAY DIFFRACTION99
2.6141-2.67090.2591670.19123636X-RAY DIFFRACTION99
2.6709-2.73310.26881720.18673705X-RAY DIFFRACTION99
2.7331-2.80140.23111940.18113523X-RAY DIFFRACTION98
2.8014-2.87710.22861790.17623597X-RAY DIFFRACTION98
2.8771-2.96180.24341980.17873677X-RAY DIFFRACTION99
2.9618-3.05730.21141850.17923578X-RAY DIFFRACTION99
3.0573-3.16660.23031820.16963658X-RAY DIFFRACTION99
3.1666-3.29330.19681670.16783644X-RAY DIFFRACTION99
3.2933-3.44310.21871670.1573700X-RAY DIFFRACTION100
3.4431-3.62460.20151970.15343637X-RAY DIFFRACTION100
3.6246-3.85150.21152140.15643645X-RAY DIFFRACTION100
3.8515-4.14870.17142090.13993672X-RAY DIFFRACTION100
4.1487-4.56580.14711890.1233666X-RAY DIFFRACTION100
4.5658-5.22550.17781720.12313715X-RAY DIFFRACTION99
5.2255-6.57980.17041830.15013719X-RAY DIFFRACTION99
6.5798-43.13660.17011890.15763718X-RAY DIFFRACTION97

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