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- PDB-5k6c: Crystal structure of prefusion-stabilized RSV F single-chain 9-10... -

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Basic information

Entry
Database: PDB / ID: 5k6c
TitleCrystal structure of prefusion-stabilized RSV F single-chain 9-10 DS-Cav1 variant.
ComponentsFusion glycoprotein F0,Fusion 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 / Resolution: 3.576 Å
AuthorsJoyce, M.G. / Zhang, B. / Lai, Y.T. / 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 1.0Oct 12, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2016Group: Structure summary

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
F: Fusion glycoprotein F0,Fusion glycoprotein F0
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3412
Polymers49,2451
Non-polymers961
Water00
1
F: Fusion glycoprotein F0,Fusion glycoprotein F0
hetero molecules

F: Fusion glycoprotein F0,Fusion glycoprotein F0
hetero molecules

F: Fusion glycoprotein F0,Fusion glycoprotein F0
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,0246
Polymers147,7353
Non-polymers2883
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area11210 Å2
ΔGint-46 kcal/mol
Surface area57730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)171.221, 171.221, 171.221
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,Fusion glycoprotein F0 / Protein F


Mass: 49245.129 Da / Num. of mol.: 1
Fragment: UNP residues 26-101 linked to residues 145-509 via LINKER residues ATGS
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), (gene. exp.) Human respiratory syncytial virus A
Strain: A2 / Production host: Homo sapiens (human) / References: UniProt: P03420
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4

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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: 4.25 Å3/Da / Density % sol: 71.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES pH 7.5, 0.19 M (NH4)2SO4, 11 % iso-propanol, 17 % 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: Jan 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.58→50 Å / Num. obs: 9782 / % possible obs: 91.5 % / Redundancy: 5.9 % / Net I/σ(I): 11.3
Reflection shellResolution: 3.58→3.71 Å / Redundancy: 1 % / % possible all: 91.2

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 3.576→49.427 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2621 464 4.75 %
Rwork0.2269 --
obs0.2287 9773 91.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.576→49.427 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3442 0 5 0 3447
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023504
X-RAY DIFFRACTIONf_angle_d0.4544754
X-RAY DIFFRACTIONf_dihedral_angle_d12.6162169
X-RAY DIFFRACTIONf_chiral_restr0.039570
X-RAY DIFFRACTIONf_plane_restr0.003597
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5756-4.09280.33771470.28833048X-RAY DIFFRACTION93
4.0928-5.15570.26361610.21473104X-RAY DIFFRACTION93
5.1557-49.43190.23711560.21583157X-RAY DIFFRACTION89
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)
11.9673-0.9834-0.11062.75891.5043.49320.37310.6773-0.4466-0.19060.2384-0.10340.94120.2256-0.49231.236-0.1598-0.1421.0054-0.11081.16067.8037-13.72275.6274
21.88460.0061.39851.91462.4115.9304-0.16650.4295-0.4377-0.1634-0.45630.84440.6266-0.69720.46251.4419-0.1805-0.32011.0295-0.22051.3561.3452-16.88133.3047
32.87760.9434-0.13827.7442.10253.3231-0.4864-0.44750.15670.28620.40620.490.39450.34980.1810.7491-0.0495-0.07290.6613-0.06160.8698.838910.259130.6659
42.5723-0.87241.38833.10690.35892.56580.29280.03430.54720.705-0.179-0.22660.12910.144-0.11430.7816-0.0669-0.05570.6680.00860.96015.897123.982633.5512
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'F' and (resid 65 through 185 )
2X-RAY DIFFRACTION2chain 'F' and (resid 186 through 309 )
3X-RAY DIFFRACTION3chain 'F' and (resid 310 through 383 )
4X-RAY DIFFRACTION4chain 'F' and (resid 384 through 509 )

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