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- PDB-5k6h: Crystal structure of prefusion-stabilized RSV F single-chain 9-10... -

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Basic information

Entry
Database: PDB / ID: 5k6h
TitleCrystal structure of prefusion-stabilized RSV F single-chain 9-10 DS-Cav1 A149C-Y458C variant.
ComponentsFusion glycoprotein F0
KeywordsVIRAL PROTEIN / Respiratory Syncytial Virus / Prefusion / Vaccine / Stabilized
Function / homology
Function and homology information


positive regulation of syncytium formation by virus / Translation of respiratory syncytial virus mRNAs / RSV-host interactions / Maturation of hRSV A proteins / Assembly and release of respiratory syncytial virus (RSV) virions / host cell Golgi membrane / Respiratory syncytial virus (RSV) attachment and entry / entry receptor-mediated virion attachment to host cell / symbiont entry into host cell / fusion of virus membrane with host plasma membrane ...positive regulation of syncytium formation by virus / Translation of respiratory syncytial virus mRNAs / RSV-host interactions / Maturation of hRSV A proteins / Assembly and release of respiratory syncytial virus (RSV) virions / host cell Golgi membrane / Respiratory syncytial virus (RSV) attachment and entry / entry receptor-mediated virion attachment to host cell / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / viral envelope / 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: 2.648 Å
AuthorsJoyce, M.G. / Zhang, B. / 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 1.0Sep 21, 2016Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
F: Fusion glycoprotein F0


Theoretical massNumber of molelcules
Total (without water)49,2171
Polymers49,2171
Non-polymers00
Water84747
1
F: Fusion glycoprotein F0

F: Fusion glycoprotein F0

F: Fusion glycoprotein F0


Theoretical massNumber of molelcules
Total (without water)147,6513
Polymers147,6513
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_663z+1,x+1,y-21
crystal symmetry operation9_474y-1,z+2,x-11
Buried area9960 Å2
ΔGint-37 kcal/mol
Surface area57340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.082, 169.082, 169.082
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number213
Space group name H-MP4132

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Components

#1: Protein Fusion glycoprotein F0 / Protein F


Mass: 49217.164 Da / Num. of mol.: 1
Fragment: UNP residues 26-103 linked to residues 145-509 via LINKER residues GS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human respiratory syncytial virus A (strain A2)
Strain: A2 / Production host: Homo sapiens (human) / References: UniProt: P03420
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O

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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: 4.1 Å3/Da / Density % sol: 69.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M phosphate-citrate, pH4.2, 0.12 M NaCl, 9.5% (w/v) PEG 8,000

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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: Jun 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.648→37.808 Å / Num. obs: 19610 / % possible obs: 79.4 % / Redundancy: 3.2 % / Net I/σ(I): 8.2

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.648→37.808 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2523 966 4.94 %
Rwork0.2216 --
obs0.2231 19566 79.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.648→37.808 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3437 0 0 47 3484
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033503
X-RAY DIFFRACTIONf_angle_d0.6234752
X-RAY DIFFRACTIONf_dihedral_angle_d15.9812177
X-RAY DIFFRACTIONf_chiral_restr0.042571
X-RAY DIFFRACTIONf_plane_restr0.003598
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.648-2.78730.31811170.30172264X-RAY DIFFRACTION69
2.7873-2.96180.31771440.28872693X-RAY DIFFRACTION83
2.9618-3.19040.26151670.26372823X-RAY DIFFRACTION86
3.1904-3.51130.25271400.2312785X-RAY DIFFRACTION84
3.5113-4.01890.25411160.21372758X-RAY DIFFRACTION82
4.0189-5.06150.21661250.18072689X-RAY DIFFRACTION79
5.0615-37.81170.24981570.21362588X-RAY DIFFRACTION73
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)
11.1197-0.06530.37941.91041.60583.37340.04170.4211-0.2893-0.27250.3539-0.08480.21490.2248-0.36040.4738-0.1208-0.03690.4729-0.0260.5051175.39326.72224.0799
24.13720.82061.12054.08941.13825.02050.47260.6907-0.9535-0.2349-0.10050.32761.8842-0.2817-0.7521.1366-0.1429-0.20330.6994-0.19590.9375172.3958308.8371-4.1187
31.44950.63330.29392.00091.62232.5147-0.03940.1349-0.1881-0.09170.0220.35440.2236-0.241-0.04780.3753-0.0176-0.05770.37830.04370.4422172.9311332.105714.3197
41.4439-0.43580.1442.0593-0.29160.83370-0.16560.10690.24940.022-0.1588-0.07870.10440.01050.411-0.00750.00880.4397-0.0420.3905175.0588356.054631.4968
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'F' and (resid 26 through 159 )
2X-RAY DIFFRACTION2chain 'F' and (resid 160 through 216 )
3X-RAY DIFFRACTION3chain 'F' and (resid 217 through 352 )
4X-RAY DIFFRACTION4chain 'F' and (resid 353 through 509 )

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