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- PDB-5k6b: Crystal structure of prefusion-stabilized RSV F single-chain 9 DS... -

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Basic information

Entry
Database: PDB / ID: 5k6b
TitleCrystal structure of prefusion-stabilized RSV F single-chain 9 DS-Cav1 variant.
ComponentsFusion glycoprotein F0
KeywordsVIRAL PROTEIN / Respiratory Syncytial Virus / Prefusion / Vaccine / Stabilized
Function / homology
Function and homology information


symbiont-mediated induction of syncytium formation / Translation of respiratory syncytial virus mRNAs / RSV-host interactions / Maturation of hRSV A proteins / Assembly and release of respiratory syncytial virus (RSV) virions / Respiratory syncytial virus (RSV) attachment and entry / host cell Golgi membrane / entry receptor-mediated virion attachment to host cell / fusion of virus membrane with host plasma membrane / viral envelope ...symbiont-mediated induction of syncytium formation / Translation of respiratory syncytial virus mRNAs / RSV-host interactions / Maturation of hRSV A proteins / Assembly and release of respiratory syncytial virus (RSV) virions / Respiratory syncytial virus (RSV) attachment and entry / host cell Golgi membrane / entry receptor-mediated virion attachment to host cell / fusion of virus membrane with host plasma membrane / viral envelope / symbiont entry into host cell / host cell plasma membrane / virion membrane / identical protein binding / plasma membrane
Similarity search - Function
Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0
Similarity search - Domain/homology
Fusion glycoprotein F0
Similarity search - Component
Biological speciesHuman respiratory syncytial virus A
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.981 Å
AuthorsJoyce, M.G. / Zhang, B. / Rundlet, E.J. / Mascola, J.R. / Kwong, P.D.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2016
Title: Iterative structure-based improvement of a fusion-glycoprotein vaccine against RSV.
Authors: Joyce, M.G. / Zhang, B. / Ou, L. / Chen, M. / Chuang, G.Y. / Druz, A. / Kong, W.P. / Lai, Y.T. / Rundlet, E.J. / Tsybovsky, Y. / Yang, Y. / Georgiev, I.S. / Guttman, M. / Lees, C.R. / ...Authors: Joyce, M.G. / Zhang, B. / Ou, L. / Chen, M. / Chuang, G.Y. / Druz, A. / Kong, W.P. / Lai, Y.T. / Rundlet, E.J. / Tsybovsky, Y. / Yang, Y. / Georgiev, I.S. / Guttman, M. / Lees, C.R. / Pancera, M. / Sastry, M. / Soto, C. / Stewart-Jones, G.B. / Thomas, P.V. / Van Galen, J.G. / Baxa, U. / Lee, K.K. / Mascola, J.R. / Graham, B.S. / Kwong, P.D.
History
DepositionMay 24, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2016Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_oper_list / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
F: Fusion glycoprotein F0
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0796
Polymers49,4731
Non-polymers6055
Water1629
1
F: Fusion glycoprotein F0
hetero molecules

F: Fusion glycoprotein F0
hetero molecules

F: Fusion glycoprotein F0
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,23618
Polymers148,4203
Non-polymers1,81615
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_645z+1,x-1,y1
crystal symmetry operation9_654y+1,z,x-11
Buried area14260 Å2
ΔGint-167 kcal/mol
Surface area53580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)171.302, 171.302, 171.302
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number213
Space group name H-MP4132
Components on special symmetry positions
IDModelComponents
11F-1002-

SO4

21F-1002-

SO4

31F-1005-

SO4

41F-1005-

SO4

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Components

#1: Protein Fusion glycoprotein F0 / Protein F


Mass: 49473.336 Da / Num. of mol.: 1
Fragment: UNP residues 26-105 linked to residues 145-509 via LINKER residues GS
Source method: isolated from a genetically manipulated source
Details: RSV F single-chain 9 DS-Cav1variant / Source: (gene. exp.) Human respiratory syncytial virus A / Strain: A2 / Production host: Homo sapiens (human) / References: UniProt: P03420
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 4.28 Å3/Da / Density % sol: 71.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M NaOAc-Acetic Acid pH 5.5, 1.09 M Li2SO4, 0.12 M MgSO4, 3.33 % (w/v) PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 25, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.98→28.94 Å / Num. obs: 17691 / % possible obs: 97.3 % / Redundancy: 4.3 % / Net I/σ(I): 11.5

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4mmu

4mmu


Resolution: 2.981→40.376 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2595 886 5.02 %RANDOM
Rwork0.2053 ---
obs0.2079 17665 97.45 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.981→40.376 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3409 0 34 9 3452
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023499
X-RAY DIFFRACTIONf_angle_d0.4994753
X-RAY DIFFRACTIONf_dihedral_angle_d10.1022153
X-RAY DIFFRACTIONf_chiral_restr0.04570
X-RAY DIFFRACTIONf_plane_restr0.003597
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9811-3.16780.3621410.30922621X-RAY DIFFRACTION93
3.1678-3.41230.31621690.24732780X-RAY DIFFRACTION100
3.4123-3.75540.27281580.21832791X-RAY DIFFRACTION99
3.7554-4.29830.21791390.18382818X-RAY DIFFRACTION99
4.2983-5.41340.23461380.1692836X-RAY DIFFRACTION98
5.4134-40.380.25911410.21182933X-RAY DIFFRACTION95
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)
11.8964-1.1903-0.04881.43171.65734.91370.29430.5581-0.7921-0.23720.29650.03091.1380.4199-0.44221.1603-0.22640.0040.7482-0.13981.0137348.7508154.8878173.5349
21.5478-0.6456-0.10161.57271.21753.5406-0.04870.2497-0.3997-0.2312-0.02770.65490.579-0.24340.02860.6799-0.0724-0.15730.5212-0.07010.7253345.5007164.3768183.8396
32.7705-0.3589-0.45545.1899-1.37372.9379-0.0594-0.07-0.15760.38410.0353-0.08410.37550.2412-0.01430.57380.0319-0.00480.6526-0.00630.5167353.9621180.696202.756
48.17090.13871.82822.5103-0.51822.01910.1446-0.49720.3220.0605-0.1040.04790.0073-0.2428-0.01480.6820.02430.04960.5442-0.08570.5471345.4314195.7199203.6125
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'F' and (resid 26 through 216 )
2X-RAY DIFFRACTION2chain 'F' and (resid 217 through 332 )
3X-RAY DIFFRACTION3chain 'F' and (resid 333 through 403 )
4X-RAY DIFFRACTION4chain 'F' and (resid 404 through 504 )

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